[gmx-users] time step in gromacs 3.3
spoel at xray.bmc.uu.se
Sat Nov 5 07:47:30 CET 2005
On Fri, 2005-11-04 at 16:01 -0600, Qing Zhu wrote:
> Hi David,
> What I did is to run 3.2.1 tpr files with 3.2.1, and run 3.3 tpr files
> with 3.3.
Try 3.2.1 tpr with 3.3
> The results of gmxcheck have hundreds of pages, and I don't know what
> could I get from gmxcheck.
See whether the difference is in the tpr or in mdrun.
If you have hundreds of page (pipe it through more) it may mean that you
are using a different force field, different coordinate/velocities which
means you can not compare the simulations.
> Qing Zhu
> David wrote:
> >On Fri, 2005-11-04 at 15:25 -0600, Qing Zhu wrote:
> >>Hi, everyone
> >>I tried to run lipid membrane simulations by setting the time step to be
> >>3 fs using gromacs-3.3, and my simulations always crashed after a short
> >>time unless I changed the time step back to 2 fs. But if I run the same
> >>lipid membrane simulations using gromacs-3.2.1, I can even use 4 fs as
> >>time step and the simulations runs fine. It is not a big problem for me,
> >>but I am just curious that why gromacs-3.3 is so critical about the time
> >>step. Any one has an idea?
> >Did you try running your 3.2.1 tpr file with 3.3 ?
> >Did you compare 3.2.1 and 3.3 tpr files (using gmxcheck)?
> >>Qing Zhu
> >>gmx-users mailing list
> >>gmx-users at gromacs.org
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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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