[gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory

[van Bemmelen]

Hi Tanping,

I don't know if that is the problem, but it could be.

I think there was (and still may be) a reproducibility issue when using
PME in GROMACS version 3.3.1 combined with FFTW3. See for instance the
maillist posts (and subsequent threads)
http://www.gromacs.org/pipermail/gmx-developers/2006-December/001986.htm
l,
http://www.gromacs.org/pipermail/gmx-developers/2007-January/001989.html
and http://www.gromacs.org/pipermail/gmx-users/2007-May/027397.html.

Some time ago I had the same problem with version 3.3.1 as you described
(simulation results changing when only changing output parameters). But
at that time I figured it was probably due to the abovementioned
PME-issue, and didn't give it much attention.

However, I'm definitely not the expert here, so I may be sending you in
a totally wrong direction. Especially since you're using the much older
3.2.1 version, of which I don't know whether it has the same issue. So I
guess my best advice to you at this moment would be to switch to the
newest version (3.3.2) first and check whether the problem persists.

Greetings,
Jeroen


>Date: Mon, 8 Oct 2007 06:07:28 -0700 (PDT)
>From: Tanping Li <jia_11_osu at yahoo.com>
>Subject: Re: [gmx-users] Different nstxout and nstvout in mdp file
>	gives	totally different trajectory
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <541778.40500.qm at web51712.mail.re2.yahoo.com>
>Content-Type: text/plain; charset=iso-8859-1
>
>Dear Jeroen,
>
>I am using gromacs-3.2.1, and PME. Is that the problem?
>
>
>Yours
>Tanping
>
>
>--- van Bemmelen
><J.J.M.vanBemmelen at student.TUDelft.NL> wrote:
>
>> Hi Tanping,
>> 
>> This may seem irrelevant, but are you using PME? And which 
>version of 
>> GROMACS is it?
>> 
>> Greetings,
>> Jeroen
>> 
>> 
>> >Date: Sun, 7 Oct 2007 08:46:04 -0700 (PDT)
>> >From: Tanping Li <jia_11_osu at yahoo.com>
>> >Subject: Re: [gmx-users] Different nstxout and
>> nstvout in mdp file
>> >	gives	totally different trajectory
>> >To: Discussion list for GROMACS users
>> <gmx-users at gromacs.org>
>> >Message-ID:
>> <288295.42898.qm at web51706.mail.re2.yahoo.com>
>> >Content-Type: text/plain; charset=iso-8859-1
>> >
>> >Dear Tsjerk,
>> >
>> >Thanks for your help.
>> >
>> >I run the two jobs on a cluster, maybe on different
>> nodes;
>> >
>> >After just a few hundreds ps, the coordinates of
>> the system
>> >differs a lot. When I calculate the distance
>> between two
>> >atoms, there is about 1.5A difference;
>> >
>> >Everything else in mdp file is exactly same.
>> >
>> >
>> >Yours
>> >Tanping