[gmx-users] on non-equilibrium MD

[Brett]

Thanks Justin.

Based on your answer, here I would like to ask,

Suppose there is a PDB for a protein-ligand, and it is already known ligand would lead extremely significant conformation change of that specific protein. Based on the protein-ligand PDB, I would like to investigate the conformation of the protein without ligand by MD.

First from the PDB for  the protein-ligand, I delete the ligand part and get the PDB for the protein part. Then with the protein part PDB and based on your lyzoyme tutorial protocol, through energy minimization, NVT and NPT equilibration, I start the production MD.

Here my question is, as for the energy of the protein in the ligand binding and ligand free state is significantly different, and based on my practice based on your lysozyme tutorial, the energy minimization, NVT and NPT equilibration steps could almost lead to no conformation change of the protein from the initial PDB conformation in the protein-ligand state, then in the production MD process, there should be a significant conformation change, which I regard that the conformation change can be checked by the energy change by command "gmx energy -f md_01.edr -o potential.xvg". If the protein conformation in the ligand binding status has much higher energy than in the ligand free state, then will you please tell me why the conformation change can only be observed in the production md process, but not in the initial energy minimization step before the production MD?

Brett










At 2016-04-02 10:21:33, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 4/1/16 10:15 PM, Brett wrote:
>> Dear All,
>>
>> For non-equilibrium MD, does it mean there would be no need for the energy
>> minimization step, NVT equilibrium step and NPT equilibrium step before the
>> production MD? In which situation we use non-equilibrium MD, and in which
>> situation we use the production MD with energy minimization step, NVT
>> equilibrium step and NPT equilibrium step?
>>
>
>The term "non-equilibrium MD" covers a lot of different possibilities, each with 
>their own applications - freezing, applying selective acceleration, pull code, 
>etc.  There is no single answer to when these should be applied because they are 
>intrinsically different.
>
>Just because there is some perturbing or net force on the system does not mean 
>you can skip all the normal preparation steps.  I can practically guarantee that 
>if you skip minimization and try to apply the pull code, your system will 
>immediately crash.  Some things are always necessary, but the exact protocol 
>depends on the goals at hand and the specific technique(s) being applied.
>
>-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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