[gmx-users] trjconv to remove periodicity (KALP15 in DPPC tutorial)

[Justin Lemkul]

On 7/10/13 8:32 AM, Atila Petrosian wrote:
> Dear Justin
>
> I do your tutorial entitled " KALP15 in DPPC ".
>
> In Step Three: Defining the Unit Cell & Adding Solvent,
>
> You said "Use trjconv to remove periodicity ".
>
> When I use trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol
> -ur compact,
> gromacs tell me: Select group for output.
>
> Which group I should select? system or dppc?
>

It doesn't really matter.  I usually stick with System, but in this case it's 
irrelevant because InflateGRO is going to nix the waters in the next step, anyway.

-Justin

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

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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