[gmx-users] gmx_ana_selcolletion_t definition

[MURILO GABARDO KRAMAR]

Thanks for your answer,

That was a detail that I didn't notice.

Another thing that I'm wondering if I'm doing right: should I use the
mappedId() or the refId() in my dynamic selection when referencing the atom
with atomnr?

2016-07-21 10:47 GMT-06:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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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