[gmx-users] restart

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 9 20:49:24 CET 2006

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!
> Yujie
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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://folding.bmc.uu.se

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