[gmx-users] RMSF per residue

[Mohsen Ramezanpour]

Hi Justin,

I have a naive question on tool development for gromacs.

If I change part of the code, or if I write a new analysis tool in c++ and
add it to this directory (after compiling with g++), shall I still
recompile the whole Gromacs again?

Cheers,
Mohsen

On Thu, May 25, 2017 at 1:43 PM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> Thanks Justin!
>
> On Thu, May 25, 2017 at 12:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 5/24/17 4:12 PM, Mohsen Ramezanpour wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I have a question on RMSF calculation:
>>>
>>> I am not sure how -res works in RMSF and I could not find any useful
>>> explanation for it.
>>>
>>> It will give the average fluctuations per residue, fine. but how exactly?
>>>
>>> 1) it calculates the RMSF for each atom in that residue first. Then, it
>>> averages over all of these atoms and reports it as the average for the
>>> residue.
>>>
>>> 2) it takes the center of mass or specific atom of the residue and
>>> calculates the RMSF for that.
>>>
>>> Or something else?
>>>
>>>
>>> I am interested in the average fluctuation for sidechain of one residue
>>> (excluding H atoms from this calculation). I want to have only one value
>>> as
>>> the average fluctuation for this group.
>>>
>>> I choose the residue-sidechain-H group (which I made in an index file)
>>> when
>>> prompted in the following command:
>>>
>>> gmx rmsf  -f  md.xtc  -fit   -s  md.tpr   -n index.ndx  -o
>>>  residues-sidechain-H.xvg  -res
>>>
>>>
>>> an alternative would be to use the following command and make an average
>>> over all atoms manually:
>>>
>>> gmx rmsf  -f  md.xtc  -fit   -s  md.tpr   -n index.ndx  -o
>>>  residues-sidechain-H.xvg
>>>
>>>
>>> The results are NOT the same as expected. I think I should use the second
>>> command and make the average manually. What do you think?
>>>
>>>
>> The total RMSF of the selection is computed, then a mass-weighted average
>> over each of the atoms is computed and that subsequent value assigned for
>> output. See the "average_residues" function in
>> src/gromacs/gmxana/gmx_rmsf.cpp
>>
>> -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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>
>
>
> --
> *Rewards work better than punishment ...*
>



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