[gmx-users] gmx_ana_selcolletion_t definition

[Justin Lemkul]

On 7/21/16 12:43 PM, MURILO GABARDO KRAMAR wrote:
> Greetings,
>
> Using version 5.1.2 of Gromacs I was able to develop the selection system
> in the proper maner. Thanks again.
>
> Now I have a new doubt about it. I ran both the VMD script that I had
> developed previously and the Gromacs code and their results differ. After
> futher investigation I've noticed that the selections handed different
> results.
>
> I guess that this two statements should be equivalent:
>
> VMD: "(within 9 of index 11776) and (name C) and (not index 11776) "
> Gromacs: ""(within 0.9 of atomnr 11776) and (name C) and (not atomnr 11776)"
>
> But running it on VMD I detect 39 atoms and when I run it on Gromacs I
> identify only 1 atom.
>
> The same occasion happens whenever I use the following selection strings:
>
> VMD: "(within 6 of index 11776) and name OW"
> Gromacs: "(within 0.6 of atomnr 11776) and name OW"
>
> This time VMD finds 1 and Gromacs finds 31.
>
> Is there anything that I didn't detect that make them different?
>

Be sure you're actually selecting the same atom.  VMD uses a zero-based index, 
so "index 11776" is actually atom number 11777.  I haven't used "atomnr" 
selection in GROMACS but I assume it is the actual atom number, as the name 
implies, starting with 1.

-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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