[gmx-users] Regarding NVT & NPT ensemble
Mark.Abraham at anu.edu.au
Tue Jan 10 15:20:20 CET 2012
On 11/01/2012 1:14 AM, ajani haresh wrote:
> Dear Sir,
> I am new user in Gromacs. I am using Gromacs for protein-ligand complex.
> If I am not wrong MD simulation have three part.
> 1. Energy Minimization
> 2. Equilibration phase
> 3. Production phase
> After EM minimization we run Equilibration using (NVT & NPT ensemble).
> I have little sily question in MD simulation.
> 1. In Protein-Ligand complex compulsory we have to run NVT & NPT
> ensemble ?
There's nothing that is required, but the advice here is fairly sound:
If your density is already correct, then NPT equilibration before NVT
simulation doesn't help anything.
> 2 shall we run without NPT ensemble MD production phase ?
Depends what you want to observe.
> 3. If we use both ensemble in production phase system might be NVPT
> like during production phase.
You cannot have an NVPT ensemble, i.e one with constant volume that is
coupled to a pressure bath.
> 4. If we run only without NPT ensemble during production phase its
> affect MD simulation ?
Yes. Only you can assess the impact on your objectives.
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