[gmx-users] RMSF per residue

[Justin Lemkul]

On 5/26/17 2:22 AM, Mohsen Ramezanpour wrote:
> 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?
>

Yes, because GROMACS functions as a single binary now (gmx).  Compiling a new 
source file will have no effect; you'll need to add the new source file to the 
list of cmake build targets so that it gets compiled and built in.

-Justin

> 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 ...*
>>
>
>
>

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

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

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