[gmx-users] Re:On the usage of g_sas

Justin Lemkul jalemkul at vt.edu
Wed Oct 9 04:43:54 CEST 2013

On 10/8/13 10:39 PM, Jernej Zidar wrote:
> Dear Justin,
>    Thanks for the help.
>    That's what the manual says about the "-f_index" switch:
> "Determine from a group in the index file what are the hydrophobic
> atoms rather than from the charge"

Ah, I see now.  I misread the initial post.  The help paragraph in g_sas made no 
mention of this feature, but it is indeed listed.

> What confuses me is that this is the only thing related to the matter,
> no word about the naming conventions. Even ol' fella Google can't find
> anything related to this issue.

Naming conventions?

I've never heard of anyone needing to use this feature, as the definition of 
hydrophobicity is generally quite robust.  I would suggest trying the default 
behavior first to determine if the result is suitable, unless you've already 
done this, in which case it would be useful to discuss if you have any 
reservations about the output you obtained.



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


More information about the gromacs.org_gmx-users mailing list