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.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
Subject: Re: [gmx-users] Regarding NVT & NPT ensemble
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4f0c4924.5020...@anu.edu.au
<mailto:4f0c4924.5020...@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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Haresh Ajani
09925522578
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========================================
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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