dpinis1 at lsu.edu
Mon Sep 27 04:52:24 CEST 2004
I have taken the .mdp file from Dr.Tielmann's website and did
work fine for 64 DPPC molecules on a monolayer and with water around.
I did not get your question "why do you have two pressure coupling
constants? What is the third?" what do you mean by this.Please clarify this
to me and suggest what to be modified and how?
You also asked me to change rvdw,the value I have now is 1.0 is 1.4 enough
or should it be more. Can I start the simulation from the point it got
crashed if yes how to do that?
I will grateful to you if you could answer me these questions.
From:gmx-users-bounces at gromacs.org on 09/26/2004 10:45 AM ZE2
Sent by: gmx-users-bounces at gromacs.org
Please respond to Discussion list for GROMACS users <gmx-users at gromacs.org>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
cc: (bcc: Dinesh Pinisetty/dpinis1/LSU)
Subject: Re: [gmx-users] md-error
On Sun, 2004-09-26 at 03:26, Dinesh Pinisetty wrote:
> Hello everybody,
> When I started of MD simulation of DPPC bilayer(96 molecules on
> monolayer) and water on either side of the monolayer for 4ns i.e. 2000000
> steps. It did run till step 166600 and then shows error as Segmentation
> fault and stopped.The Warnings are as follows:
> Warning: 1-4 interactions between 6501 and 6506 at distance larger than
> turn on -debug for more information
> Step 166599 Warning: pressure scaling more than 1%, mu: 1.01263
> Step 166600 Warning: pressure scaling more than 1%, mu: 1.07707 1.07707
> Wrote pdb files with previous and current coordinates
> Segmentation fault
> This is the error it has shown.What might be the mistake and how to sort
> I have viewed the .xtc file till step 166600 it was fine,but
> it crashed.If I sort the mistake by anyones suggestion can I continue
> the point it had crashed,if so how to do it.
> Any suggestions would be greatly helpful to me.
> By the way my .mdp file is attached to this mail.Please check this out
> so that mistake can be identified by any of you.
Check the box dimensions during the simulation (using g_energy). You may
need to have a large VDW cut-off because the lipid head (charge) groups
are very large.
> I hopw you will do the needful.
> Thanking you,
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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