[gmx-users] Temperature or Pressure Coupling

[sun]

Thank You Sir. I have another question? What should be the ideal time for NPT run? My question might sound trivial but i need to know if this makes a difference. I want to simulate protein for 50ns. So, prior to final mdrun, how long NPT run is required?


Sent from my iPhone

> On 26-Jan-2016, at 4:49 pm, "VITALY V. CHABAN" <vvchaban at gmail.com> wrote:
> 
> yes
> 
> 
> 
>> On Tue, Jan 26, 2016 at 3:42 AM, sun <sun.iba2 at gmail.com> wrote:
>> 
>> Hello
>> I want to simulate a protein in water and observe its behavior alone and
>> then in the presence of ligand. I have read somewhere that NPT MD is best
>> for pro-lig complexes as it resembles the in vitro and in vivo conditions
>> (conformational changes,biomolecular reactions, binding etc.). So My
>> question is whether I should use NpTMD for protein alone as well? Or if
>> anyone could give some good reference.
>> Regards
>> Suniba
>> 
>> Sent from my iPhone
>> Sent from my iPhone
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