[gmx-users] Protein-Protein distance

[Justin Lemkul]

On 1/5/16 4:11 PM, Life Sciences Inc wrote:
> I am little confued to use the gmx distance command specifically for my
> purpose mentioned in my question ;
>
> gmx distance -f file.xtc -s file.gro -n file.ndx
>
> for outputting the distance between protein 1 and protein 2, protein 1 and
> protein 3 , protein 1 and protein 4 I will use -oav or -oxyz or -oall
> option ?and how can I calculate the distance between the proteins with
> center of mass of my selection which I am providing though index file?
>

http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0#g_dist

Read the help description to see which of the available output options you need; 
they all provide slightly different content.  If you just want the total 
distance, use -oall, for the (x,y,z) components, use -oxyz.

The actual selection string you need to pass to -select (or choose 
interactively, as would be the case for the command you have shown) depends on 
what the groups are named/numbered in the index file.

If you have, e.g. groups "protein1" and "protein2":

gmx distance -f file.xtc -s file.gro -n file.ndx -selet 'com of group "protein1" 
plus com of group "protein2"'

-Justin

>
>
> On Tue, Jan 5, 2016 at 5:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/5/16 1:18 AM, Life Sciences Inc wrote:
>>
>>> Dear Gromacs Users
>>>
>>> Kindly let me know how to calculate the protein protein distance as a
>>> function of time with gromacs. I want to calculate the distance based on
>>> the center of mass of the selection which is CA atoms. I have 4 proteins
>>> in
>>> the system and want to calculate the distances as distance between Protein
>>> 1 and Protein 2, then Protein 1 and Protein 3 , then Protein 1 and Protein
>>> 4.
>>>
>>>
>>> I used gmx mindist command but it cannot be used to calculate distance
>>> with
>>> center of mass, I tried gmx distance also, but do not know how to use it
>>> for my above mentioned purpose.
>>>
>>>
>> gmx distance is the correct command, but you haven't told us what you've
>> tried and why it didn't work (or why you think it didn't work), so it's not
>> productive for us to simply guess.
>>
>> -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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-- 
==================================================

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

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