[gmx-users] restart
David van der Spoel
spoel at xray.bmc.uu.se
Thu Feb 9 22:07:13 CET 2006
Viswanadham Sridhara wrote:
> 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.
How about nstlist? Is it set to 1?
>
>
>
> On 2/9/06, *Yujie Wu* <yujie.wu at hec.utah.edu
> <mailto: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 <mailto:spoel at xray.bmc.uu.se>
> spoel at gromacs.org <mailto:spoel at gromacs.org> http://folding.bmc.uu.se
> >
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> >
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> _______________________________________________
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>
>
> --
> Viswanadham Sridhara,
> Graduate Research Assistant,
> Old Dominion University, "VIRGINIA".
>
>
> ------------------------------------------------------------------------
>
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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://xray.bmc.uu.se/~spoel
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