[gmx-users] (no subject)

[abhijit Kayal]

Thanks Justin for the help. But if I want to look the dipole auto
correlation or hydrogen bond dynamics ... is that possible?


On Fri, Feb 28, 2014 at 4:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/28/14, 5:38 AM, abhijit Kayal wrote:
>
>> Dear Gromacs users,
>>
>>         My system contained CNT+ water. I have created a dynamically
>> index.ndx file
>> which contain the number of water molecules in each frame inside cnt.
>> Now I want to study the dipole orientation of these water molecules. But I
>> can't select all the groups at a time. From the mailing lists search I
>> came
>> to know that any gromacs analysis tools can't do this. So is there any
>> other way to do these type of analysis. I am using gromacs 4.5.5.
>>
>>
> You have to analyze each frame individually rather than processing the
> trajectory in one pass.  With a simple shell script, you can loop through
> the index groups, write out a corresponding frame from the trajectory, then
> analyze it.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur