[gmx-users] a question related to gmx energy minimization

[Brett]

Dear Justin,
 
I mean why the RMSD is such huge. Does it mean in the energy mminimization step the protein has moved from point A to point B which is long long distance away from point A but, although the protein has been continously embedded in water? If the RMSD is above several thousands, it would mean the protein conformation after energy minimization would be absolutely different from the input pdb for the pdb2gmx.
 
I am looking forward to getting a clarification.
 
Brett

 




At 2015-04-27 00:00:22, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 4/26/15 9:53 AM, Brett wrote:
>> Dear Tsjerk,
>>
>> Will you please explain to me why the RMSD in this step is so large? For this reason I think there is something wrong.
>>
>
>No, there's nothing wrong; the analysis in this case is meaningless.
>
>Energy minimization inherently makes large (orders of magnitude in many cases) 
>changes to the potential as the structure is relaxed.  An average energy over 
>the course of this process has absolutely no physical meaning.
>
>-Justin
>
>-- 
>==================================================
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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
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>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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