[gmx-users] Re: trjconv for pbc

[Justin Lemkul]

On 11/2/13 12:25 PM, rankinb wrote:
> Here are the steps that I used:
>
> 1.  trjconv -pbc whole -dump 37.875
> 2.  trjconv -pbc nojump
> 3.  trjconv -center
> 4.  g_select to make an index containing the atoms of interest
> 5.  trjconv to extract coordinates
>
> Regardless of whether step 1 is used or not, the resulting coordination
> shell configuration is not complete in the sense that it looks like the
> figure I posted previously.  In all steps, I used the same .tpr file...is it
> possible that I need to generate a new one after step 1?
>

1. trjconv -center -pbc mol -dump 37.875

As long as you're choosing an appropriate index group here (i.e., the single 
solute molecule of interest), you should not need any further invocations of 
trjconv before extracting coordinates.  Pop open the resulting coordinate file 
in your favorite visualization software and verify.  It should be very obvious 
if it worked as expected.

2. Make selection
3. Extract

-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
20 Penn St.
Baltimore, MD 21201

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

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