spoel at xray.bmc.uu.se
Sun Sep 26 10:45:42 CEST 2004
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 each
> 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 2nm
> turn on -debug for more information
> Step 166599 Warning: pressure scaling more than 1%, mu: 1.01263 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 it
> I have viewed the .xtc file till step 166600 it was fine,but unfortunately
> it crashed.If I sort the mistake by anyones suggestion can I continue from
> 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 once
> so that mistake can be identified by any of you.
why do you have two pressure coupling constants? What is the third?
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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