[gmx-users] how can we control output ?

[Justin Lemkul]

On 8/14/13 9:43 AM, Albert wrote:
> Hello:
>
>   I am producing MD production with command:
>
> mpirun -np 24 mdrun_mpi -plumed plumed.dat -s md.tpr -v -g md.log -x md.xtc -o
> md.trr -e md.edr
>
> I notice that it generate two additional files:
>
> HILLS COLVAR
>
> the output in this two files are very frequent such as:
>
> #! FIELDS time cv1 cv2 vbias
>      0.0000     -1.372322679      0.467140973    0.000000000
>      0.0900     -1.225425363      0.486899137    0.029999999
>      0.1800     -1.420091748      0.546218574    0.031921782
>      0.2700     -1.430565715      0.584925413    0.057605527
>      0.3600     -1.193568826      0.524875879    0.056731977
>      0.4500     -1.215992570      0.439122081    0.074018419
>      0.5400     -1.320514202      0.395002633    0.059704699
>      0.6300     -1.247566938      0.493606031    0.119831786
>      0.7200     -1.258976460      0.403684765    0.120678633
>
> AND:
>       0.090     -1.225425363      0.486899137      0.086999997 0.086999997
> 0.061249998 1.960
>       0.180     -1.420091748      0.546218574      0.086999997 0.086999997
> 0.061201861 1.960
>       0.270     -1.430565715      0.584925413      0.086999997 0.086999997
> 0.060562217 1.960
>       0.360     -1.193568826      0.524875879      0.086999997 0.086999997
> 0.060583858 1.960
>       0.450     -1.215992570      0.439122081      0.086999997 0.086999997
> 0.060157006 1.960
>       0.540     -1.320514202      0.395002633      0.086999997 0.086999997
> 0.060510237 1.960
>       0.630     -1.247566938      0.493606031      0.086999997 0.086999997
> 0.059040397 1.960
>       0.720     -1.258976460      0.403684765      0.086999997 0.086999997
> 0.059019958 1.960
>       0.810     -1.331293344      0.531644762      0.086999997 0.086999997
> 0.059053400 1.960
>       0.900     -1.477816820      0.541284800      0.086999997 0.086999997
> 0.059861982 1.960
>
>
> I am performing 200 ns MD simulations. The file probably will become too big....
> I am just wondering how can we setup the frequency record for the HILL and
> COLVAR file?
>

I would suggest asking PLUMED questions on the PLUMED forum.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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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