[gmx-users] regarding group selection in output

[Justin Lemkul]

On 7/4/14, 12:57 AM, RINU KHATTRI wrote:
> hello every one now i am in
>
> trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact
>
> this command but in out put they are asking
>
> Will write gro: Coordinate file in Gromos-87 format
> Reading file em.tpr, VERSION 4.5.5 (single precision)
> Reading file em.tpr, VERSION 4.5.5 (single precision)
> Select group for output
> Group     0 (         System) has 14036 elements
> Group     1 (          Other) has  6656 elements
> Group     2 (           POPC) has  6656 elements
> Group     3 (          Water) has  7380 elements
> Group     4 (            SOL) has  7380 elements
> Group     5 (      non-Water) has  6656 elements
>
>   i am unable to understand which group to select
>
> is this command is ok or i have to use set of command to center or
> jump the ligand
>

The command appears to be the same as in my membrane protein tutorial, so I'm 
assuming you're doing the same thing (although you're not working with the 
tutorial because trjconv says you have POPC, not DPPC, as the command 
indicates).  Regardless, if you're preparing the system, you should be saving 
the entire system.  Only saving a subset of atoms is most common for 
post-processing after a simulation.

-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

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