[gmx-users] restart

[Yujie Wu]

> 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?

This is where the problem is at least for my test. When nstlist is set to 1, no
difference any more. Thanks to all.

Yujie


> 
> > 
> > 
> >  
> > 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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> > 
> > 
> > 
> > -- 
> > 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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