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 <
ansu...@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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