GENESIS  tutorial  3  REMD	
 Lecturer: Takaharu Mori
2017/03/01

Contents	 I. Temperature  REMD  simulation  of  alanine  tripeptide  in  water	
	

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Preparation  of  the  initial  structure	
Energy  minimization	
Equilibration  for  T-­‐‑REMD	
Production  run  of  T-­‐‑REMD	
Analysis  of  T-­‐‑REMD  trajectories	

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Pressure  REMD	
Surface-­‐‑tension  REMD	
Hamiltonian  REMD  (Replica-­‐‑exchange  umbrella  sampling)	
2D-­‐‑REMD  (T-­‐‑REMD/H-­‐‑REMD)	

	II. How  to  do  other  types  of  REMD?	
	Basic  usage	
 In  this  tutorial,  we  use  not  only  spdyn  but  also  analysis tools!
in  the  install  directory.
# enter the login node!
$ ssh -l userXX riken.eastus.cloudapp.azure.com!
!
# enter a computational node (n001-n017)!
$ ssh nXXX!
!
# Run spdyn using hybrid MPI/OpenMP!
# Note that each node has 24 CPU cores!
$ export OMP_NUM_THREADS=3!
$ mpirun –np 8 /home2/data/genesis/bin.CPU.dp/spdyn INP!
!
# Run analysis tools (do not use mpirun)!
$ /home2/data/genesis/bin.CPU.dp/some_analysis INP!

Part  I	 Temperature REMD simulation of alanine tripeptide in waterOverall  ﬂow  of  T-­‐‑REMD  simulations	 Initial  structure
T  =  300K
Energy  	
minimization	&	pre-­‐‑equilibration	
in  NPT  at  300K  1atm

Equilibration  	
in  NVT  at  individual  temperature	T  =  400K

T-­‐‑REMD  in  NVT  production  run…

v To  prevent  the  vaporization  of  solvent  at  higher  temperatures,  we  usually  use  the  NVT  ensemble  in  T-­‐‑REMD.  	

T  =  310K

v Note  that  replicas  in  high  temperature  have  high  pressure,  which  can  also  enhance  the  structural  sampling.
Analysis

How  many  CPU  cores  we  need?	
 Now,  we  want  to  use  m  CPU  cores  in  one  replica  and  n  replicas  in  total.	
n  replicas…

m  CPU  cores	=  #  of  MPI  processors  ×  #  of  OpenMP  threads
We  need  m  ×  n  CPU  cores  in  total  to  perform  REMD  in  GENESIS
In  this  tutorial,  we  use  6  replicas  due  to  limitation  of  the  available  CPUs.	
(1  replica  =  4  CPUs  with  1  OpenMP  thread)  Preparation  	
 $ cd Tutorial_3!
$ ls!
Part1 Part2!
!
$ cd Part1!
$ ls!
0_setup2_pre-equilibration
1_minimize
3_equilibration

4_production!
5_analysis !

In  Part  I,  we  will  change  the  directory  	from  0_setup  to  5_analysis  step  by  stepStep0.  Preparation  of  the  initial  structure	 Our  target  system:  Alanine  tripeptide  in  TIP3P  water	
We  use  CHARMM  C36  force  ﬁeld
# change directory!
$ cd 0_setup!
!
$ ls!
top_all36_prot.rtf
wbox.pdb!
par_all36_prot.prm
wbox.psf
toppar_water_ions.str!

Number  of  protein  atoms:  42	Number  of  water  molecules:    9250

PDB,  PSF,  Parameter  and  topology  ﬁles  are  already  prepared.

Step1.  Energy  minimization	 We  carry  out  5,000-­‐‑steps  energy  minimization  with  the  steepest  descent  method,	
where  the  positional  restraints  are  applied  on  the  protein  heavy  atoms.  
[INPUT]!
topfile = ../0_setup/top_all36_prot.rtf# topology file!
parfile = ../0_setup/par_all36_prot.prm# parameter file!
strfile = ../0_setup/toppar_water_ions.str # stream file!
psffile = ../0_setup/wbox.psf# protein structure file!
pdbfile = ../0_setup/wbox.pdb# PDB file!
reffile = ../0_setup/wbox.pdb# PDB file for restraints!
!
[OUTPUT]!
dcdfile= step1.dcd# DCD trajectory file!
rstfile= step1.rst# restart file!
!
[MINIMIZE]!
method= SD# Steepest descent method!
nsteps= 5000# number of minimization steps!
eneout_period= 100# energy output period!
crdout_period= 100# coordinates output period!
rstout_period= 5000# restart output period!
!
[SELECTION]!
group1= sid:PROA and heavy!
!
[RESTRAINTS]!
nfunctions= 1# number of functions!
function1= POSI# restraint function type!
direction1= ALL# direction!
constant1= 1.0# force constant!
select_index1= 1# restrained groups!

Step2.  Pre-­‐‑equilibration	
 NVT  MD  with  posres                      è  NPT  MD  with  posres                  è  NPT  MD  without  posres  [INPUT]!
rstfile = ../1_minimize/step1.rst!
!
[OUTPUT]!
dcdfile = step2.1.dcd!
rstfile = step2.1.rst!
!
[DYNAMICS]!
integrator= LEAP!
nsteps= 5000!
!
[ENSEMBLE]!
ensemble= NVT!
tpcontrol= LANGEVIN!
temperature= 300.00!
!
[SELECTION]!
group1= sid:PROA and heavy!
!
[RESTRAINTS]!
nfunctions= 1!
function1= POSI!
direction1= ALL!
constant1= 1.0!
select_index1 = 1!

[INPUT]!
rstfile = step2.1.rst!
!
[OUTPUT]!
dcdfile = step2.2.dcd!
rstfile = step2.2.rst!
!
[DYNAMICS]!
integrator= LEAP!
nsteps= 5000!
!
[ENSEMBLE]!
ensemble= NPT!
tpcontrol= LANGEVIN!
temperature= 300.00!
pressure= 1.0!
isotropy= ISO!
!
[SELECTION]!
group1= sid:PROA and heavy!
!
[RESTRAINTS]!
nfunctions= 1!
function1= POSI!
direction1= ALL!
constant1= 1.0!
select_index1 = 1!

[INPUT]!
rstfile = step2.2.rst!
!
[OUTPUT]!
dcdfile = step2.3.dcd!
rstfile = step2.3.rst!
!
[DYNAMICS]!
integrator= LEAP!
nsteps= 5000!
!
[ENSEMBLE]!
ensemble= NPT!
tpcontrol= LANGEVIN!
temperature= 300.00!
pressure= 1.0!
isotropy= ISO!
!
!

We  gradually  equilibrate  the  system  by  vanishing  the  restrains  and  switching  the  ensembles.

Step3.  Equilibration  at  each  temperature	 At  Step3,  we  can  use  the  REMD  module  in  GENESIS,  where  REMD  without  replica  exchange  is  performed.
[INPUT]!
rstfile = ../2_pre-equilibration/step2.3.rst!
!
[OUTPUT]!
dcdfile = step3_rep{}.dcd!
rstfile = step3_rep{}.rst!
remfile = step3_rep{}.rem!
logfile = step3_rep{}.log!
!
[ENERGY]!
forcefield= CHARMM!
Replica  index  is  electrostatic= PME!
switchdist= 10.0!
automatically  cutoffdist= 12.0!
inserted  into  {}  pairlistdist= 13.5!
!
of  the  output  [DYNAMICS]!
ﬁlename.
integrator= LEAP!
nsteps= 5000!
timestep= 0.002!
eneout_period=
10!
crdout_period=
100!
rstout_period= 5000!
!
[CONSTRAINTS]!
rigid_bond= YES# use SHAKE/SETTLE!

[ENSEMBLE]!
ensemble
tpcontrol
temperature!
[REMD]!
dimensionexchange_period
type1
nreplica1
parameters1= NVT!
= LANGEVIN!
= 300.00!

=!
= 0
= !
=!
=!

# no parameter exchange!

v In  GENESIS,  REMD  can  be  achieved  by  just  adding  the  [REMD]  section  in  the  control  ﬁle  for  a  conventional  MD.	
Let’s  edit  the  [REMD]  section!

Prepare  replica  temperatures	 We  prepare  temperatures  to  be  used  in  REMD  by  utilizing  the  temperature  generator  server  (hfp://folding.bmc.uu.se/remd/)
Exchange  probability  of  0.2-­‐‑0.3  is  supposed  to  realize  eﬃcient  structural  sampling  in  REMD.	

We  use  SETTLE  and  SHAKE  for  bond  constraint	

The  estimated  temperatures  are  	
300.00,  301.81,  …,  …,  501.46  (90  replicas!)	
	è  We  select  ﬁrst  6  temperatures  in  this  tutorial.

Control  ﬁle  for  equilibration	 [INPUT]!
rstfile = ../2_pre-equilibration/step2.3.rst!
!
[OUTPUT]!
dcdfile = step3_rep{}.dcd!
rstfile = step3_rep{}.rst!
remfile = step3_rep{}.rem!
logfile = step3_rep{}.log!
!
[ENERGY]!
forcefield= CHARMM!
electrostatic= PME!
switchdist= 10.0!
cutoffdist= 12.0!
pairlistdist= 13.5!
!
[DYNAMICS]!
integrator= LEAP!
nsteps= 5000!
timestep= 0.002!
eneout_period=
10!
crdout_period=
100!
rstout_period= 5000!
!
[CONSTRAINTS]!
rigid_bond= YES!

[ENSEMBLE]!
ensemble
tpcontrol
temperature!
[REMD]!
dimensionexchange_period
type1
nreplica1
parameters1= NVT!
= LANGEVIN!
= 300.00!

= 1!
= 0# no parameter exchange!
= temperature!
= 6!
= 300.00 302.53 305.09 ¥!
307.65 310.24 312.85!

Submibing  a  job	 In  GENESIS,  number  of  CPU  cores  per  replica  is  automatically  determined  by  dividing  total  number  of  CPU  cores  by  total  number  of  replicas.  	
NCPUs/replica  =  Ntotal  CPUs  /  Nreplicas
speciﬁed  by  a  commandspeciﬁed  in  the  control  ﬁle$ export OMP_NUM_THREADS=1!
$ mpirun –np 24 /home2/data/genesis/bin.CPU.dp/spdyn step3.inp!

CPU:

0	
 

1	
 

2	
 

3	
 

4	
 

5	
 

6	
 

7	
 

Replica1	
 Replica2	
 step3_rep1.dcd!
step3_rep1.rst!
step3_rep1.rem!
step3_rep1.log

step3_rep2.dcd!
step3_rep2.rst!
step3_rep2.rem!
step3_rep2.log

8	
 

9	
 

10	
 

11	
 

Replica3	
 

…

12	
 

13	
 

14	
 

15	
 

Replica4	
 

16	
 

17	
 

18	
 

19	
 

Replica5	
 

20	
 

21	
 

22	
 

23	
 

Replica6	 Trajectory  ﬁles  are  output  from  each  replica.

Let’s  submit  a  job!

Step4.  Production  run  of  REMD	 To  perform  a  production  run,  we  just  modify  the  previous  control  ﬁle  for  the  equilibration  run.
[INPUT]!
rstfile = ../3_equilibration/step3_rep{}.rst!
!
[OUTPUT]!
dcdfile = step4_rep{}.dcd!
rstfile = step4_rep{}.rst!
remfile = step4_rep{}.rem!
logfile = step4_rep{}.log!
!
[ENERGY]!
forcefield= CHARMM!
electrostatic= PME!
switchdist= 10.0!
cutoffdist= 12.0!
pairlistdist= 13.5!
!
[DYNAMICS]!
integrator= LEAP!
nsteps= 5000!
timestep= 0.002!
eneout_period=
10!
crdout_period=
100!
rstout_period= 5000!
!
[CONSTRAINTS]!
rigid_bond= YES!

[ENSEMBLE]!
ensemble
tpcontrol
temperature!
[REMD]!
dimensionexchange_period
type1
nreplica1
parameters1= NVT!
= LANGEVIN!
= 300.00!

= 1!
= 500!
= temperature!
= 6!
= 300.00 302.53 305.09 ¥!
307.65 310.24 312.85!

In  this  example,  replica  exchange  is  afempted  every  500  steps.

Let’s  edit  [REMD]  section  and	
submit  a  production  job!

log  information	
 REMD> Step:
500
Dimension:
Replica
ExchangeTrial
1
1 >
0
N
2
2 >
3
A
3
3 >
2
A
4
4 >
0
N
Parameter:
300.000
303.630
RepIDtoParmID:
1
3
ParmIDtoRepID:1
3

1

ExchangePattern:
AcceptanceRatio
0 /
0
1 /
1
1 /
1
0 /
0
301.810305.470!
2
4!
2
4

REMD> Step:
1000
Dimension:
Replica
ExchangeTrial
1
1 >
2
A
2
3 >
4
R
3
2 >
1
A
4
4 >
3
R
Parameter:
301.810303.630
RepIDtoParmID:
2
3
ParmIDtoRepID:
3
1

1

ExchangePattern:
AcceptanceRatio
1 /
1
0 /
1
1 /
1
0 /
1
300.000
305.470!
1
4!
2
4

2! T2-­‐‑T3,  T4-­‐‑T5,  T6-­‐‑T7,…  pairs
BeforeAfter!
300.000
300.000!
301.810303.630!
303.630301.810!
305.470305.470!

1! T1-­‐‑T2,  T3-­‐‑T4,  T5-­‐‑T6,…  pairs
BeforeAfter!
300.000
301.810!
303.630
303.630!
301.810300.000!
305.470305.470!

T1

T2

T3

T4

  500  step:

300.00301.81

303.63305.471000  step:

300.00301.81

303.63305.471500  step:

300.00301.81

303.63305.47…

log  information	
 REMD> Step:
500
Dimension:
Replica
ExchangeTrial
1
1 >
0
N
2
2 >
3
A
3
3 >
2
A
4
4 >
0
N
Parameter:
300.000
303.630
RepIDtoParmID:
1
3
ParmIDtoRepID:1
3

1

ExchangePattern:
AcceptanceRatio
0 /
0
1 /
1
1 /
1
0 /
0
301.810305.470!
2
4!
2
4

2!
Before300.000
301.810303.630305.470

After!
300.000!
303.630!
301.810!
305.470!

REMD> Step:
1000
Dimension:
Replica
ExchangeTrial
1
1 >
2
A
2
3 >
4
R
3
2 >
1
A
4
4 >
3
R
Parameter:
301.810303.630
RepIDtoParmID:
2
3
ParmIDtoRepID:
3
1

1

1!
Before300.000
303.630301.810305.470

After!
301.810!
303.630!
300.000!
305.470!

ExchangePattern:
AcceptanceRatio
1 /
1
0 /
1
1 /
1
0 /
1
300.000
305.470!
1
4!
2
4

After  long  REMD  run,  “Acceptance  ratio”  will  get  close  to	the  value  that  was  speciﬁed  in  the  REMD  temperature  generator.

log  information	
 REMD> Step:
500
Dimension:
Replica
ExchangeTrial
1
1 >
0
N
2
2 >
3
A
3
3 >
2
A
4
4 >
0
N
Parameter:
300.000
303.630
RepIDtoParmID:
1
3
ParmIDtoRepID:1
3

1

ExchangePattern:
AcceptanceRatio
0 /
0
1 /
1
1 /
1
0 /
0
301.810305.470!
2
4!
2
4

2!
Before300.000
301.810303.630305.470

REMD> Step:
1000
Dimension:
Replica
ExchangeTrial
1
1 >
2
A
2
3 >
4
R
3
2 >
1
A
4
4 >
3
R
Parameter:
301.810303.630
RepIDtoParmID:
2
3
ParmIDtoRepID:
3
1

1

1!
Before300.000
303.630301.810305.470

ExchangePattern:
AcceptanceRatio
1 /
1
0 /
1
1 /
1
0 /
1
300.000
305.470!
1
4!
2
4f(T1)  =  Replica3
Eq  (5)  in  the  Sugita  &  Okamoto  paper:	
Chem.  Phys.  Lef.,  314  (1999)  141–151  After!
300.000!
303.630!
301.810!
305.470!

Permutation  function

f−1(Replica3)  =  T1

After!
301.810!
303.630!
300.000!
305.470!

Analyze  log  information  1	
 Time  courses  of  the  replica  index  which  has  T1  =  300K:$ cd ~/Part1/5_analysis/1_replica_index!
!
$ grep “ParmIDtoRepID:” ../../4_production/log > replica_id.log!
!
$ gnuplot!
gnuplot> set terminal x11!
gnuplot> plot [][0:7] ’replica_id.log’ u 0:2!

gnuplot  is  installed  in  the  login  node  only!  To  display  the  plot  data  by  gnuplot,  login  the  node  with  –X  option.	

(ref)  Sugita  &  Okamoto	                  Chem.  Phys.  Lef.,  314  (1999)  141–151  Analyze  log  information  2	
 Time  courses  of  the  temperature  and  potential  energy  in  Replica  1$ cd ~/Part1/5_analysis/2_temperature_energy!
!
$ grep "Parameter:" ../../4_production/log > parameter.log!
!
$ grep “INFO:” ../../4_production/step4_rep1.log > rep1.log!
!
$ gnuplot!
gnuplot> set terminal x11!
gnuplot> plot ‘parameter.log’ u 0:3 with lines!
gnuplot> plot ‘rep1.log’ u 3:5 with lines!

(ref)  Sugita  &  Okamoto	                  Chem.  Phys.  Lef.,  314  (1999)  141–151  Output  ﬁles  	
 In  the  REMD  simulations,  the  following  ﬁles  are  generated  from  each  replica.
ü step4_repX.dcd:!
!
ü step4_repX.rem:!
!
ü step4_repX.log:!
!
ü step4_repX.rst:!

Coordinates  trajectory		Parameter  index		Energy  log  in  each  replica	Restart  ﬁle  including  the  last  coordinates,  velocities,  replica  parameter  index,  etc.	

Note  that  dcdﬁle  and  energy  logﬁle  contain  “mixed  coordinates  and  energies  at  diﬀerent  temperatures”  		è  We  need  to  sort  the  information  by  temperature  to  analyze  the  trajectories  at  the  focusing  temperature.

Sorting  the  coordinates  (4  replicas  case)	
 1

Replica  1

Replica  2

Replica  3

Replica  4

2

7

8

9

10

11

12

18

21

22

24

3

3

4

T2

3

2

T2

25

T4

T3

1

T1

2

23

T3

2

T3

20

T2

4

3

19

4

T4

4

4

17

4

T4

T4

16

T4

1

T3

15

T1

1

3

14

T3

T1

2

13

3

T2

dcdfileremfile62

dcdfileremfile5

T2

1

dcdfileremfile4

T1

dcdfileremfile

3

T1

1

1

2

Sorting  by  T1
1
dcdfile

2

3
T1

4

5

6

7

8
T1

9

10

11

12

13
T1

14

15

16

17

18

19
T1

20

21

22

23
T1

24

25

Convert  REMD  trajectory	 [INPUT]!
psffile = ../0_setup/wbox.psf# protein structure file!
reffile = ../0_setup/wbox.pdb# PDB file!
dcdfile = ../4_production/step4_rep{}.dcd# DCD trajectory file!
remfile = ../4_production/step4_rep{}.rem# replica exchange ID file!
!
[OUTPUT]!
pdbfile = step4.pdb# output PDB file!
trjfile = step4_parm{}.dcd# output trajectory file!
!
[SELECTION]!
group1 = all!
!
[FITTING]!
fitting_method = NO!
!
1[OPTION]!
check_only= NO!
convert_type= PARAMETER!
convert_ids= 1# (empty = all)!
dcd_md_period = 100# coordinates output period!
trjout_format = DCD# (PDB/DCD)!
trjout_type= COOR+BOX# (COOR/COOR+BOX)!
trjout_atom= 1# output atom selection!
pbc_correct= NO# (wrap molecules)T   =  300.00K$ cd ~/Part1/5_analysis/3_remd_convert!
$ /home2/data/genesis/bin.CPU.dp/remd_convert INP > log!

Further  analysis	 After  the  trajectory  is  converted,  we  analyze  the  trajectories	
in  more  details,  for  example,  		• End-­‐‑to-­‐‑end  distance  of  the  peptide		• Dihedral  angle  of  the  backbone  atoms	
	• Principal  component  analysis	
• Free  energy  proﬁle	Part  II	 Other REMD simulations

REMD  functions  in  GENESIS	 In  Part  I,  	
we  learned  how  to  perform  Temperature  REMD  in  the  NVT  ensemble  	
	GENESIS  can  employ  various  types  of  REMD  methods:		• Temperature  REMD  in  the  NPT  ensemble	
• Pressure  REMD  in  the  NPT  ensemble	
• Surface-­‐‑tension  REMD  in  the  NPγT  ensemble  (for  biomembranes)	
• Hamiltonian  REMD  (restraint  potential  exchange)	
• 2D-­‐‑REMD  (T-­‐‑REMD/P-­‐‑REMD)	
• 2D-­‐‑REMD  (T-­‐‑REMD/H-­‐‑REMD)
In  Part  II,  we  learn  how  to  edit  the  control  ﬁle  	for  various  type  of  REMD  in  GENESIS.

Preparation	 $ cd Tutorial_3!
$ ls!
Part1 Part2!
!
$ cd Part2!
$ ls!
ExamplePractice2
Practice1
Practice3

Practice4
Practice5

Practice6!
Practice7!

In  Part  II,  we  will  change  the  directory  	from  Practice1  to  Practice7  step  by  step.	
(Diﬃculty  is  gradually  increased!)Example	 Temperature  REMD  in  the  NVT  ensemble  (Tutorial  I)	using  4  replicas  with  T  =  300,  310,  320,  330K	
NVT

NVT
[ENSEMBLE]!
ensemble
tpcontrol!
[REMD]!
dimensionexchange_period
type1
nreplica1
parameters1

Tm

T n

= NVT!
= LANGEVIN!

= 1!
= 500!
= temperature!
= 4!
= 300.0 310.0 320.0 330.0!

Level:  ★☆☆☆☆

Practice  1  	
 Temperature  REMD  in  the  NPT  ensemble  at  P  =  1atm	
(isotropic  pressure  coupling)  using  4  replicas  with  T  =  300,  310,  320,  330K	
NPT
P  =  1atm	

Tm

NPT
P  =  1atm	

T n

[ENSEMBLE]!
ensemble
tpcontrol________________!
[REMD]!
dimensionexchange_period
type1
nreplica1
parameters1= ____!
= LANGEVIN!
= _!
= ___!

= 1!
= 1000!
= temperature!
= 4!
= 300.0 310.0 320.0 330.0!

Hints:	
• [ENSEMBLE]  section  is  modiﬁed	
• Step2.2  and  2.3  in  Part  I	
• See  User  manual  p.42-­‐‑44	Level:  ★★☆☆☆

Practice  2  	
 Pressure  REMD  in  the  NPT  ensemble  at  T  =  300K	
(isotropic  pressure  coupling)  using  4  replicas  with  P  =  1,  10,  100,  1000atm	
NPT

NPT

T  =  300K

T  =  300K

Pm

Pn

[ENSEMBLE]!
ensemble
tpcontrol___________________!
[REMD]!
dimensionexchange_period
type1
nreplica1
parameters1= ___!
= LANGEVIN!
= ___!
= ___!

= 1!
= 500!
= ________!
= 4!
= ___ ___ ___ ___!

Hints:	•   [ENSEMBLE]  and  [REMD]  sections  should  be  modiﬁed	
• Step2.2  and  2.3  in  Part  I	
• See  User  manual  P.54

Level:  ★★☆☆☆

Practice  3  	
 Surface-­‐‑tension  REMD  in  the  NPγT  ensemble  at  T  =  300K  and  Pn  =  1atm	
(semi-­‐‑isotropic  pressure  coupling)  using  5  replicas  with  γ  =  -­‐‑10,  -­‐‑5,  0,  5,  10dyn/cm	
NPγT
T  =  300K	
P  =  1atm

γm

NPγT
T  =  300K	
P  =  1atm

γn[ENSEMBLE]!
ensemble
tpcontrol________________________!
[REMD]!
dimensionexchange_period
type1
nreplica1
parameters1= ____!
= LANGEVIN!
= ___!
= _!
= _______!

= 1!
= 500!
= _____!
= 5!
= ___ ___ ___ ___ ___!

Level:  ★★★☆☆

Practice  4  	 Two-­‐‑dimensional  T-­‐‑REMD/P-­‐‑REMD		[ENSEMBLE]!
Temperature:  	ensemble	300,  310,  320,  330,  340K  (5  replicas)	
tpcontrol
Pressure:    	!
	1,  10,  100,  1000atm  (4  replicas)  isotropic  pressure  coupling	 [REMD]!
dimension	
exchange_period
5  x  4  =  20  replicas  in  total	

T1
P1
pressure

P2
P3
P4

T2

temperature

T3

T4

T5

type1
nreplica1
parameters1!
?!
!

= ___!
= LANGEVIN!

= !
= 500!
= !
= !
= !

Level:  ★★★★☆

Practice  5  	 Restraint-­‐‑potential  REMD  (REUS)  in  the  NVT  ensemble  using  4  replicas,  where  we  apply  distance  restraints  (3,  4,  5,  and  6  Å  with  k  =  10  kcal/mol/Å2)  	
between  C  atom  in  Residue  1    and  N  atom  in  Residue  3	
C  (Residue  1)

N  (Residue  3)

dm
dn

Exchange  the  target  distance	
of  the  distance  restraint	[ENSEMBLE]!
ensemble
tpcontrol
temperature!
[SELECTION]!
group1group2!
[RESTRAINTS]!
nfunctions
function1
select_index1
constant1
reference1!
[REMD]!
dimensionexchange_period
type1
nreplica1
rest_function1= NVT!
= LANGEVIN!
= 300.00!

= an:__ and ________!
= an:__ and ________!

= 1!
= DIST!
= 1 2!
= ___ ___ ___ ___!
= ___ ___ ___ ___!

= 1
= 500
= ___________!
= 4!
= _!

!

Common  to  conventional  MD  with  distance  restraint

Level:  ★★★★★

Practice  6  	 Restraint-­‐‑potential  REMD  (REUS)  in  the  NVT  ensemble  using  4  replicas,  where  we  apply  dihedral  angle  restraints  on  φ and ψ of Residue  2	(φ,ψ)  =  (180,  180),  (170,  170),  (160,  160),  (150,  150)  with  k  =  10  kcal/mol/Å2  	
φ =C-N-CA-C
ψ =N-CA-C-N

φm, ψmExchange  the  target  two  dihedral  angles	

φn, ψn[ENSEMBLE]!
ensemble
tpcontrol
temperature!
[SELECTION]!
group1:!
[RESTRAINTS]!
nfunctions
function1
select_index1
constant1
reference1
function2
select_index2
constant2
reference2!
[REMD]!
dimensionexchange_period
type1
nreplica1
rest_function1= NVT!
= LANGEVIN!
= 300.00!

= an:__ and ________!
:!

= _!
= ____!
= 1 2 3 4!
= ___ ___ ___ ___!
= ___ ___ ___ ___!
= ____!
= 2 3 4 5!
= ___ ___ ___ ___!
= ___ ___ ___ ___!

= 1
= 500
= ___________!
= 4!
= _ _!

!

Level:  ★★★★★

Practice  7  	
 Two-­‐‑dimensional  T-­‐‑REMD/REUS	
in  the  NVT  ensemble	

Temperature:  		300,  310,  320,  330,  340K	
Restraints:  		distance  restraints  (3,  4,  5,  and  6  Å  with  k  =  10  kcal/mol/Å2)	
  	
between  Cα  atoms  (atom  name  CA)		
in  Residue  No.  1  and  3		
5  x  4  =  20  replicas  in  total	

T1d1
distance  restraint

d2
d3
d4

T2

temperature

T3

T4

T5

[ENSEMBLE]!
ensemble= NVT!
tpcontrol= LANGEVIN!
temperature= 300.00!
!
Hint: Practice 4 + Practice 5!

References	
 Appendix	 Level:  ★☆☆☆☆

Practice  1  	
 Temperature  REMD  in  the  NPT  ensemble  at  P  =  1atm	
(isotropic  pressure  coupling)  using  4  replicas  with  T  =  300,  310,  320,  330K	
NPT
P  =  1atm	

Tm

NPT
P  =  1atm	

T n

[ENSEMBLE]!
ensemble
tpcontrolpressure
isotropy!
[REMD]!
dimensionexchange_period
type1
nreplica1
parameters1= NPT!
= LANGEVIN!
= 1!
= ISO!

= 1!
= 1000!
= temperature!
= 4!
= 300.0 310.0 320.0 330.0!

Hints:	
• [ENSEMBLE]  section  is  modiﬁed	
• Step2.2  and  2.3  in  Part  I	
• See  User  manual  p.42-­‐‑44	Level:  ★★☆☆☆

Practice  2  	
 Pressure  REMD  in  the  NPT  ensemble  at  T  =  300K	
(isotropic  pressure  coupling)  using  4  replicas  with  P  =  1,  10,  100,  1000atm	
NPT

NPT

T  =  300K

T  =  300K

Pm

Pn

[ENSEMBLE]!
ensemble
tpcontrol
temperatureisotropy!
[REMD]!
dimensionexchange_period
type1
nreplica1
parameters1= NPT!
= LANGEVIN!
= 300!
= ISO!

= 1!
= 500!
= pressure!
= 4!
= 1 10 100 1000!

Hints:	•   [ENSEMBLE]  and  [REMD]  sections  should  be  modiﬁed	
• Step2.2  and  2.3  in  Part  I	
• See  User  manual  P.54

Level:  ★★☆☆☆

Practice  3  	
 Surface-­‐‑tension  REMD  in  the  NPγT  ensemble  at  T  =  300K  and  Pn  =  1atm	
(semi-­‐‑isotropic  pressure  coupling)  using  5  replicas  with  γ  =  -­‐‑10,  -­‐‑5,  0,  5,  10dyn/cm	
NPγT
T  =  300K	
P  =  1atm

γm

NPγT
T  =  300K	
P  =  1atm

γn[ENSEMBLE]!
ensemble
tpcontrol
temperaturepressure
isotropy!
[REMD]!
dimensionexchange_period
type1
nreplica1
parameters1= NPgT!
= LANGEVIN!
= 300!
= 1!
= SEMI-ISO!

= 1!
= 500!
= GAMMA!
= 5!
= -10 -5 0 5 10!

Level:  ★★★☆☆

Practice  4  	 Two-­‐‑dimensional  T-­‐‑REMD/P-­‐‑REMD		[ENSEMBLE]!
Temperature:  	ensemble	300,  310,  320,  330,  340K  (5  replicas)	
tpcontrol
Pressure:    	!
	1,  10,  100,  1000atm  (4  replicas)  isotropic  pressure  coupling	 [REMD]!
dimension	
exchange_period
5  x  4  =  20  replicas  in  total	

T1
P1
pressure

P2
P3
P4

T2

temperature

T3

T4

T5

type1
nreplica1
parameters1
type2
nreplica2
parameters2!
!
!

= NPT!
= LANGEVIN!

= 2!
= 500!
= temperature!
= 5!
= 300 310 320 330 340!
= pressure!
= 4!
= 1 10 100 1000!

Level:  ★★★★☆

Practice  5  	 Restraint-­‐‑potential  REMD  (REUS)  in  the  NVT  ensemble  using  4  replicas,  where  we  apply  distance  restraints  (3,  4,  5,  and  6  Å  with  k  =  10  kcal/mol/Å2)  	
between  C  atom  in  Residue  1    and  N  atom  in  Residue  3	
C  (Residue  1)

N  (Residue  3)

dm
dn

Exchange  the  target  distance	
of  the  distance  restraint	[ENSEMBLE]!
ensemble
tpcontrol
temperature!
[SELECTION]!
group1group2!
[RESTRAINTS]!
nfunctions
function1
select_index1
constant1
reference1!
[REMD]!
dimensionexchange_period
type1
nreplica1
rest_function1= NVT!
= LANGEVIN!
= 300.00!

= an:C and rno:1!
= an:N and rno:3!

Common  to  conventional  MD  with  distance  restraint= 1!
= DIST!
= 1 2!
= 10 10 10 10!
= 3 4 5 6!

= 1
= 500
= RESTRAINT!
= 4!
= 1!

!

Level:  ★★★★★

Practice  6  	 Restraint-­‐‑potential  REMD  (REUS)  in  the  NVT  ensemble  using  4  replicas,  where  we  apply  dihedral  angle  restraints  on  φ and ψ of Residue  2	(φ,ψ)  =  (180,  180),  (170,  170),  (160,  160),  (150,  150)  with  k  =  10  kcal/mol/Å2  	
φ =C-N-CA-C
ψ =N-CA-C-N

φm, ψmExchange  the  target  two  dihedral  angles	

φn, ψn[ENSEMBLE]!
ensemble
tpcontrol
temperature[SELECTION]!
group1group2group3group4group5!
[RESTRAINTS]!
nfunctions
function1
select_index1
constant1
reference1
function2
select_index2
constant2
reference2!
[REMD]!
dimensionexchange_period
type1
nreplica1
rest_function1= NVT!
= LANGEVIN!
= 300.00!
= an:C and rno:1!
= an:N and rno:2!
= an:CA and rno:2!
= an:C and rno:2!
= an:N and rno:3!

= 2!
= DIHED!
= 1 2 3 4!
= 10 10 10 10!
= 180 170 160 150!
= DIHED!
= 2 3 4 5!
= 10 10 10 10!
= 180 170 160 150!

= 1
= 500
= RESTRAINT!
= 4!
= 1 2!

!

Level:  ★★★★★

Practice  7  	
 Two-­‐‑dimensional  T-­‐‑REMD/REUS	
in  the  NVT  ensemble	

Temperature:  		300,  310,  320,  330,  340K	
Restraints:  		distance  restraints  (3,  4,  5,  and  6  Å  with  k  =  10  kcal/mol/Å2)	
  	
between  Cα  atoms  (atom  name  CA)		
in  Residue  No.  1  and  3		
5  x  4  =  20  replicas  in  total	

T1d1
distance  restraint

d2
d3
d4

T2

temperature

T3

T4

T5

[ENSEMBLE]!
ensemble
tpcontrol
temperature!
[SELECTION]!
group1group2!
[RESTRAINTS]!
nfunctions
function1
select_index1
constant1
reference1!
[REMD]!
dimensionexchange_period
type1
nreplica1
parameters1
type2
nreplica2
rest_function2!
!

= NVT!
= LANGEVIN!
= 300.00!

= an:CA and rno:1!
= an:CA and rno:3!

= 1!
= DIST!
= 1 2!
= 10 10 10 10!
= 3 4 5 6!

= 2!
= 500!
= temperature!
= 5!
= 300 310 320 330 340!
= RESTRAINT!
= 4!
= 1!