[gmx-users] Regarding NVT & NPT ensemble

[Mark Abraham]

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: 
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation. 
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.

Mark