[gmx-users] restart

[David van der Spoel]

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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> 
> 
> 
> -- 
> 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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