[gmx-users] RMSD analysis

[Justin Lemkul]

On 6/6/17 1:11 PM, RAHUL SURESH wrote:
> Dear Justin
> 
> Thank you. I am considering  Rmsd rmsf rg as just supplementary analysis
> for my study.  My aim to analyse  conformational change in protein. I would
> like to bring a note on protein stability after ligand binding. I don't
> know to which part of monomer I can compare the rmsd of complex with.
> First 50ns or last .. can you please help me with this?

I'm not following.  You're talking about monomers and time intervals as if 
they're interchangeable.  What's the story?  Do you have a multimer?  Are you 
curious about demonstrating convergence?

-Justin

> On Tue, 6 Jun 2017 at 5:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
>>
>>
>> On 6/6/17 2:12 AM, RAHUL SURESH wrote:
>>> Dear Users
>>>
>>> *Exp procedure:*
>>> I have simulated the protein monomer for 150ns. Using the 150ns
>> conformer,
>>> ligand is docked to the protein using autodock and the simulation is
>>> carried out for 50ns.
>>>
>>> *Analysis:*
>>>
>>> Is it possible to compare my RMSD, RMSF, ROG analysis of complex system
>>> with that of monomer? If yes which part of the monomer trajectory should
>> be
>>> considered.?
>>>
>>
>> This is up to you to determine in light of whatever your goals are in
>> running
>> the simulation.  What are you trying to test or determine?  Unless the
>> protein's
>> stability is seriously impacted by the ligand, RMSD and Rg are useless.
>> RMSF
>> might be useful if there are motions that are amplified or damped by ligand
>> binding.  Run the analysis and see what happens on a per-residue basis.
>>
>> -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

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