[gmx-users] use of " -t nvt.cpt" option in NPT equilibration

[Justin Lemkul]

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 
introducing discontinuities.

Rule of thumb: preserve the previous ensemble unless you have a very good reason 
to ignore or re-create it.

-Justin

>
> Regards,
> Vijayan.R
>
> On Tue, Sep 9, 2014 at 4:38 PM, Ansuman Biswas <
> ansuman at physics.iisc.ernet.in> wrote:
>
>> Hi,
>>    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,
>> regards,
>> ansuman
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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