[gmx-users] Re: trjconv for pbc

[Justin Lemkul]

On 11/2/13 11:23 AM, rankinb wrote:
> Tsjerk,
>
> Thanks for your reply.  I have tried using the center option, but ran into
> similar problems.  Here are the exact commands that I used:
>
> g_select -f file.xtc -s file.tpr -n index.ndx -select 'group 14 and within
> 0.71 of group 13' -b 37.875 -e 37.875 -on index1 (where group 14 contains
> the water molecules and group 13 is the solute molecule)
>
> trjconv -s file.tpr -n index1.ndx -f file.xtc -o out.gro -b 37.875 -e 37.875
>
> trjconv -f out.gro -s file.tpr -n index.ndx -o out2.gro -center
>
> Does this procedure seem reasonable?
>

Right commands, wrong order.

1. Center on the solute
2. Make selection
3. Extract coordinates

Note that specifying -b and -e with the same time can fail in some cases; use 
-dump instead.

-Justin

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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