[gmx-users] g_dist as an alternative for g _saltbr

[Justin Lemkul]

On 10/17/14 4:49 PM, Diogo Martins de Sá wrote:
> That can certainly work for me! Especially because I know my groups
> "functional groups". I guess if one was still in doubt what to focus on,
> then my idea could still be useful (with a bit more of work).
>
> Now, just so I get things right:
>
> 1. I got to make ONE group in my .ndx that contains all my functional
> groups, and use trjconv to create a trajectory containing only those
> groups.
> 2. Same goes for .tpr
>

Correct.

> 3. When I run g_saltbr I should use -sep, correct? or else I'm going to
> have problems viewing the distanceXtime graphics of all SBs using
> xmgrace.
>

Probably a good idea to write everything separately.

> 4. Is the -t option measured in nm? Making the default 1um (micrometer)?
> If so, then I should change it from 1000 to 0.4?

Yes, Gromacs always uses nm as the default distance unit.  The default behavior 
basically says "consider everything possible."

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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