[gmx-users] (no subject)

[Justin Lemkul]

On 2/28/14, 6:36 AM, abhijit Kayal wrote:
> Thanks Justin for the help. But if I want to look the dipole auto
> correlation or hydrogen bond dynamics ... is that possible?
>

Each frame is just a time point in the trajectory.  Concatenate the individual 
output and you get a time series.

-Justin

>
> 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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>
>
>

-- 
==================================================

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

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