[gmx-users] Regarding NVT & NPT ensemble

[Justin A. Lemkul]

ajani haresh wrote:
> 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.
> 

The two ensembles work in concert to produce the final ensemble that is used 
during data collection.  NVT relaxes the system such that the temperature is 
stable and you are obtaining values in the correct distribution.  You pass that 
output to NPT to preserve previous state information and begin a new ensemble, 
which now maintains temperature and stabilizes the pressure.

For some systems, you could probably bypass NVT and go straight to NPT 
equilibration; the exact procedure depends on how robust your system is.  The 
progression of NVT -> NPT -> data collection is common and intuitive, by not 
necessarily the only way to proceed.

-Justin

> Thanks in advance
>  
> 
>     Message: 6
>     Date: Wed, 11 Jan 2012 01:20:20 +1100
>     From: Mark Abraham <Mark.Abraham at anu.edu.au
>     <mailto: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
>     <mailto:gmx-users at gromacs.org>>
>     Message-ID: <4F0C4924.5020205 at anu.edu.au
>     <mailto: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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> 
> 
> 
> -- 
> -----------------------------------------------------------------
> Haresh Ajani
> 09925522578
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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