[gmx-users] How to add multiple simulations?

[Justin Lemkul]

On 7/21/14, 8:37 AM, Batdorj Batsaikhan wrote:
> Dear
>
> when I concatenate 5 different *.xtc files, came from following outputs.
>
> command
>
> trjcat -o md50.xtc -n ../index.ndx -f ../md*.xtc
>
> ************************************************************************************************
>
>            File                Start time       Time step
> ---------------------------------------------------------
>              ../md_0_1.xtc        0.000 ps        5.000 ps
>      ../md_0_2.xtc        0.000 ps        5.000 ps WARNING: same Start time as
> previous
>              ../md_0_3.xtc        0.000 ps        5.000 ps WARNING: same Start
> time as previous
>              ../md_0_4.xtc        0.000 ps        5.000 ps WARNING: same Start
> time as previous
>              ../md_0_5.xtc        0.000 ps        5.000 ps WARNING: same Start
> time as previous
>
> Reading frame     0 time    0.000
> Last frame       2000 time 10000.000
> Reading frame       0 time    0.000
> Last frame       2000 time 10000.000
> Reading frame       0 time    0.000
> Last frame       2000 time 10000.000
> Reading frame       0 time    0.000
> Last frame       2000 time 10000.000
> Reading frame       0 time    0.000
>
> Continue writing frames from ../md_0_5.xtc t=0 ps, frame=0
> Last frame       2000 time 10000.000    ->  frame   2000 time 10000.000 ps
>
> Last frame written was 2000, time 10000.000000 ps
>
> gcq#348: "Sitting on a rooftop watching molecules collide" (A Camp)
>
> ********************************************************************************************************
>
> Is there any error?
>
> I thought that final xtc file might be 10000 time frame and 50 ns.
>

If you're trying to concatenate multiple simulations that all start from the 
same time (in this case, zero), you need to use the -settime option to modify 
the time values, otherwise trjcat defaults to overwriting the frames with later 
instances of the same time.

-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

==================================================