[gmx-users] Protein-Protein distance

[Life Sciences Inc]

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?



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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