[gmx-users] obtaining .gro timeframe

[Justin Lemkul]

On 7/1/14, 8:53 PM, Chetan Mahajan wrote:
> Dear All,
>
> I need some help to generate .gro file corresponding to a given timeframe
> of the trajectory obtained in gromacs MD run.
>
> Currently, I am using following command to generate a .gro timeframe (5000
> ps) from .xtc trajectory:
>
>
> *trjconv -f lnanop.xtc -o time5000.gro -s lnanop.tpr -dump 5000*
>
> where lnanop.tpr is generated by following command at the beginning of the
> MD run which geenrates above .xtc file:
>
> grompp -f $sethome/prod_lnanopff16.mdp -c $b4prod/lnanop.gro -p
> $sethome/outff18-2_aftermin.top -o lnanop.tpr -n $sethome/index18-2.ndx
>
> where each file means by what is implied by its extension.
>
> Now, the comparison of input file to grompp and time0.gro (initial)
> timeframe generated by "trjconv" command on .xtc looks good. However, there
> are some differences between the files lnanop.gro (generated at the end of
> the gromacs MD run) and that generated from "trjconv" command to extract
> last timeframe of the same xtc trajectory, *although files match on many
> other accounts. Some of the output of -diff command on two files in the
> following*:
>
> @@ -2322,8 +2322,8 @@
>      55SOL    HW1 2320   3.174   0.144   7.460
>      55SOL    HW2 2321   3.041   0.201   7.382
>      56SOL     OW 2322   0.015   1.114   1.210
> *-   56SOL    HW1 2323  -0.031   1.076   1.130 *
> *-   56SOL    HW2 2324  -0.040   1.096   1.292 *
> *+   56SOL    HW1 2323   3.191   1.076   1.130*
> *+   56SOL    HW2 2324   3.182   1.096   1.292*
>      57SOL     OW 2325   1.398   3.388  10.246
>      57SOL    HW1 2326   1.471   3.321  10.236
>      57SOL    HW2 2327   1.365   3.388  10.341
>
> - : for .gro file at the end of gromacs MD run
> + : for .gro timeframe file obtained from .xtc trajectory ( using trjconv):
> that with no signs, is the common part of the two files
>
> What's happening? Please comment. Thanks a lot!
>

Periodicity.  The final configuration is "made whole" and atoms are put in the 
box such that they have positive coordinates.  The frames within the .xtc file 
are not whole and not corrected for any particular convention.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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