[gmx-users] Re: gmx-users Digest, Vol 93, Issue 52

[ajani haresh]

Thanks Sir,

But I have one more question.

If I run first NVT then NPT ensemble. So we get output file from NPT
ensemble.

NPT ensemble output we will use into production phase.

Means they also take parameter from NVT ensemble.

Thanks in advance


> Message: 6
> Date: Wed, 11 Jan 2012 01:20:20 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Regarding NVT & NPT ensemble
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F0C4924.5020205 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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
>
>
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> End of gmx-users Digest, Vol 93, Issue 52
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>



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Haresh Ajani
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