Hi,
There are no settings that matter in particular for pulling compared to a
normal simulation.
All the settings that matter normally matter here as well.
NVT pulling should give nearly identical results no NPT,
as long as you set the volume correctly.
Berk
To: gmx-users@gromacs.org
Subject: Re : [gmx-users] PULL CODE AND NpT ensemble
Date: Thu, 27 Aug 2009 08:03:56 -0400
From: gigita...@aol.fr
Hi Berk,
Thanks for your answer. I just want to be sure that the procedure is correct.
No I do not look at the pressure/volume fluctutation. But I do want to make a
clever choice of the ensemble so that no significant extra artifact are
generated, since the number of contraint to be calculated is not negligible. I
previously used no P coupling and I was wondering is that feature could explain
that the average force plot is not smooth function. Other criteria such as
Cut-off value for LJ and coulomb may also be checked out?
Geraldine
-----E-mail d'origine-----
De : Berk Hess <g...@hotmail.com>
A : Discussion list for GROMACS users <gmx-users@gromacs.org>
Envoyé le : Jeudi, 27 Août 2009 13:45
Sujet : RE: [gmx-users] PULL CODE AND NpT ensemble
Hi,
I would use v-rescale and Berendsen pressure coupling.
Although Berendsen pressure coupling, strictly speaking, does not give the
correct ensemble,
in practice it produces negligible artifacts, unless you are looking at
pressure/volume fluctuations.
Berk
To: gmx-users@gromacs.org
Date: Thu, 27 Aug 2009 07:20:00 -040
0
From: gigita...@aol.fr
Subject: [gmx-users] PULL CODE AND NpT ensemble
Hi all,
I would like to use pull code to evaluate the free energy of pulling system1
from system2. Free energy calculation should be done for NpT ensemble. All
tutorials found for calculating free energy used
1) berensen for T and P coupling or
2) berensen for T coupling AND Parrinelo for P coupling or
3)Vrescale for T and no P coupling
I am a bit lost in which one should lead to real ensemble.
Is any one could help?
Regards,
geraldine, phD
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