[gmx-users] GMX5.0 g_select

[Justin Lemkul]

On 3/7/15 3:18 PM, xy21hb wrote:
>
>
>
> Dear Gmxers,
>
> What I meant is to use the result of  "g_select" as index to calculate e.g. g_hbond,
> Since if I simply use "-n" the g_select index, it will give the selected water in each frame.
> But then how I can average them in gromacs automatically?
>

Each index group from g_select can be used to analyze the matching frame in the 
trajectory.  So you need to analyze each frame separately, concatenate the 
output, and average.  If you assemble a text file (.xvg) that g_analyze can 
read, that's one way, otherwise scripting something to calculate an average is 
trivial.

-Justin

> Thanks,
>
> Yao
>
>
>
>
>
>
>
> At 2015-03-07 06:27:49, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>> Yes, it can. I suspect that's even one of the examples in the selection
>> help.
>>
>> Mark
>> On 06/03/2015 3:43 pm, "xy21hb" <xy21hb at 163.com> wrote:
>>
>>> Dear GMXers,
>>>>
>>>>
>>>> I wonder if g_select in GMX5.0 can select some distance e.g. 5A of the
>>> solvent e.g. water w.r.t. a protein dynamically,since different numbers of
>>> the solvent in each time frame should be observed.
>>>
>>> Thanks,
>>>
>>>
>>> Yao
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-- 
==================================================

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

==================================================