[gmx-users] restart

Viswanadham Sridhara muta.mestri at gmail.com
Thu Feb 9 21:56:22 CET 2006


Hi,
I might be wrong here.
But please check the exact end time in the .gro output files you mentioned.
The beginning of both the files should have t=.......even if there is a step
difference (dt=0.002ps), there can be a 3rd decimal change in the output
files of co-ordinates, velocities...etc.



On 2/9/06, Yujie Wu <yujie.wu at hec.utah.edu> wrote:
>
> > Yujie Wu wrote:
> > > Hi,
> > >
> > > I am wondering why in gromacs a restarted MD simulation will not
> reproduce the
> > > trajectory by a continuous one.
> > >
> > > The test I did was to run a 4-step MD and got the final .gro file.
> Then ran a
> > > 2-step MD, generating the tpr using "tpbconv -s -f -e -extend", then
> ran it and
> > > got the final .gro file. A diff of the two .gro files tells me that
> they are
> > > different even in the third decimal place. The `nstxout', `nstvout',
> `nstfout',
> > > and `nstenergy' variables were set to 1. The Gromacs version is 3.3(single
> > > precision).
> > >
> > > Any idea where and what the problem is? Thanks in advance.
> > >
> > are you sure these simulations did the same number of steps? Please
> check!
>
> Thanks. I just double-checked. They had the same number of steps.
>
> Yujie
>
> > > Yujie
> > >
> > >
> > >
> > > _______________________________________________
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> >
> >
> > --
> > David.
> > ________________________________________________________________________
> > 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://folding.bmc.uu.se
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--
Viswanadham Sridhara,
Graduate Research Assistant,
Old Dominion University, "VIRGINIA".
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