[gmx-users] Query- RMSD

[Justin Lemkul]

On 4/7/15 8:20 AM, Priya Das wrote:
> Can you comment more on it?
> Should i increase the time for simulation?
>

Put simply, analyzing RMSD on its own tells you very little.  You should assess 
convergence of the results based on any physical properties that are of 
interest.  That's all for you to decide.  Why are you doing the simulations? 
What do you know about the biology?  What do you expect to see, and do you see 
it?  What is the time scale of the relevant dynamics?

Reducing the vast amount of information from a simulation to just RMSD over 10 
ns is inadequate to address anything useful.

-Justin

> On Tue, Apr 7, 2015 at 4:16 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
>> No.
>>
>> Cheers,
>>
>> Tsjerk
>> On Apr 7, 2015 12:16 PM, "Priya Das" <priyadas001 at gmail.com> wrote:
>>
>>> Dear all,
>>>
>>> For checking ligand interactions with protein , i generated a RMSD plot
>> for
>>> ligand. The simulations were done for 10 ns. Has the system converged?
>>>
>>> ​
>>>
>>> --
>>> *Let us all join hands to save our " Mother Earth"*
>>> ------------------------------------------------------------------------
>>> Regards,
>>> Priya Das
>>> Research Scholar
>>> Dept. of Computational Biology and Bioinformatics,
>>> University of Kerala
>>>
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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

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