[gmx-users] use of " -t nvt.cpt" option in NPT equilibration
jalemkul at vt.edu
Tue Sep 9 23:41:21 CEST 2014
On 9/9/14 5:09 PM, R.S.K.Vijayan wrote:
> Hi Ansuman,
> That is optional.
Generally speaking, no, it's not. The real truth lies in what the .mdp settings
are and what the intent of NPT is. If you don't pass the .cpt file to grompp
-t, you stand to lose much (or all) of the previous state information, thus
Rule of thumb: preserve the previous ensemble unless you have a very good reason
to ignore or re-create it.
> On Tue, Sep 9, 2014 at 4:38 PM, Ansuman Biswas <
> ansuman at physics.iisc.ernet.in> wrote:
>> Can someone please explain if it is necessary to use the -t flag during
>> NPT equilibration?
>> The following command is mentioned in the lysozyme tutorial:
>> $ grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
>> whereas , I have found the command without the -t flag in another tutorial:
>> grompp -v -f npt.mdp -c protein-NVT.gro -p protein.top -o protein-NPT.tpr
>> Thanking in advance,
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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