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Subject: RE: [NWCHEM] Shake algorithm
Date: Thu, 13 Jul 2006 10:46:18 -0700
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Thread-Topic: [NWCHEM] Shake algorithm
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From: "Vorpagel, Erich R" <Erich.Vorpagel@pnl.gov>
To: "Vasiliy S. Znamenskiy" <znamensk@sci.ccny.cuny.edu>
Cc: <nwchem-users@emsl.pnl.gov>
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Here are you answers:

1) yes by default, they can be turned off with "noshake solute" for
example

2) yes, see 1)

3) yes there is an importance to the order.  The best I can recommend is
to include any keyword directives in the prepare and other task modules
in the order in which they appear in the documentation. I have found
that usually works.

4) vreass is "Velocity reassignment" which applies a random velocity to
all atoms in a Boltzmann distribution at the temperature specified.
This can happen only once, or repeatedly every so many steps.  Your
example sets the temperature to zero degrees Kelvin each step, which is
then followed by the shake algorithm that causes the hydrogen atoms to
jump to position.

5) I suspect a link between two segments where a bond is supposed to be
is not being created.  I suspect there is an error in the fragment file
or you need to add a specific LINK command in the prepare module to
create the bond.

6) Check in the literature for papers by T.P. Straastma.  I don't have
the references available to me right now.

7) I have not used the isotherm anneal option so I don't know.

Hope this helps,

Erich Vorpagel
 

-----Original Message-----
From: owner-nwchem-users@emsl.pnl.gov
[mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of Vasiliy S.
Znamenskiy
Sent: Thursday, July 13, 2006 7:41 AM
To: nwchem-users@emsl.pnl.gov
Subject: [NWCHEM] Shake algorithm

Hi,
I have many questions about MD:

1)	Does Shake algorithm work both in the dynamics and in 
the optimize MD simulations?
2)	Does Shake algorithm is executed by default? Then to do 
free hydrogen atoms bonded to frozen heavy atoms is it necessary to
include "noshake" directive.
3) 	Is there a some influence of an order of directives 
inside the same one MD block (which directive is first, second and so
on) onto MD simulation? 

4) What is execution algorithm of "vreass" directive? When I try to
apply "wreass 1 0.0" to freeze atom randomize moving, some atoms
(hydrogen) do jumping dancing, however printing temperature shows zero.

5) Is there some distance limit for harmonic bond force? I observe when
bonded atoms are moved onto big interatomic distance they lose theirs
bond force. They are looking as not bonded. Or MD program change
topology during execution?

6) Where is it possible to read about details of NWCHEM MD algorithm?
Where are total descriptions of precise meanings of various terms used
in user manual?

7) I found "isotherm anneal" directive doesn't work. Am I right? If not,
what is execution algorithm of "annealing"?