[gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory

[David van der Spoel]

Tanping Li wrote:
> Dear Tsjerk,
> 
> Thanks for your help.
> 
> I run the two jobs on a cluster, maybe on different
> nodes;
> 
> After just a few hundreds ps, the coordinates of the
> system differs a lot. When I calculate the distance
> between two atoms, there is about 1.5A difference;
> 
> Everything else in mdp file is exactly same.
> 
Have you checked the following:

gmxcheck -s1 top1.tpr -s2 top2.tpr
and verified that only the output parameters were different?

If so, please submit a bugzilla and upload the two tpr files.
> 
> Yours
> Tanping
> 
> 
>  
> 
> --- Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 
>> Hi Tanping Li,
>>
>> Can you be more elaborate? What are the differences?
>> What do you mean with
>> "totally different"? Did you run it on the same
>> machine? Was everything else
>> the same?
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On 10/5/07, Tanping Li <jia_11_osu at yahoo.com> wrote:
>>> Dear all,
>>>
>>> I run a 1ns trajectory for a protein in water. by
>>> accidence, I find that the minor different in mdp
>> file
>>> gives two totally different trajectories. By
>> setting
>>> nstxou=500
>>> nstvou=500;
>>>
>>> and
>>>
>>> nstxou=2500
>>> nstvou=2500;
>>>
>>> There is very large difference between two
>>> trajectories (dt=2fs in both cases). I am really
>>> confused: nstxou JUST sets the frequency to output
>> the
>>> coordinate, why I get different results? Looking
>>> forward to your opinion and thanks a lot.
>>>
>>> Yours
>>> Tanping Li
>>> _______________________________________________
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>>
>> -- 
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se