[gmx-users] Protein-Protein distance

[Life Sciences Inc]

I want to ask one question regarding using gmx distance in the script, I
was able to calculate distances the way you told me Justin, command doesn't
run with gmx distance on gromacs 5.0.5 when I load intel version of
gromacs, it runs like gmx_mpi distance but when I am using this in a bash
script its not working. Can anyone help me with this? I need to run
multiple distance commands that's why I want to make a script.

Thanks

On Tue, Jan 5, 2016 at 10:45 PM, Life Sciences Inc <
contact.lifesciences.inc at gmail.com> wrote:

> OK , Thanks a lot now I got  it , if I feel any difficulty further I will
> ask.
>
> Thank you
>
>
>
> On Wed, Jan 6, 2016 at 2:42 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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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>>>> Gromacs Users mailing list
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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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>
>