[gmx-users] RE: Is non-linear data output/storage possible?

[Justin Lemkul]

On 7/11/13 3:14 PM, Neha wrote:
> Hi everybody,
>
> I started changing init-step. Now I seem to have another problem. When I go
> to switch to another 'block' it tells me that my input and checkpoint states
> are not identical when I use mdrun the second time. I am not sure how they
> can be any different as I only have one .cpt file in the directory.
>

The .cpt file stores information related to output frequency.  The existing .cpt 
file designates output every X steps, while the new .tpr file specifies output 
every Y steps, and X != Y, so mdrun complains.  I'm assuming mdrun aborts at 
that point?  Have you tried with -noappend?

> My list of commands is right here -
>
> grompp -f 1step.mdp -c 315monolayer.gro -p dppc_monolayer.top -o
> 315monolayer.tpr
>
> mdrun -nt 4 -s 315monolayer.tpr -c 315monolayer.gro -e 315monolayer.edr -o
> 315monolayer.trr -x 315monolayer.xtc -g 315monolayer.log -cpo
> 315monolayer.cpt -rdd 2.5
>
> grompp -f 10step.mdp -c 315monolayer.tpr -p dppc_monolayer.top -o
> 315monolayer.tpr -t 315monolayer.cpt
>
> mdrun -nt 4 -s 315monolayer.tpr -c 315monolayer.gro -e 315monolayer.edr -o
> 315monolayer.trr -x 315monolayer.xtc -g 315monolayer.log -cpi
> 315monolayer.cpt -cpo 315monolayer.cpt -rdd 2.5
>

Save yourself some typing :)

mdrun -nt 4 -deffnm 315monolayer

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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