[gmx-users] extention of the simulation
Justin A. Lemkul
jalemkul at vt.edu
Sat May 19 13:52:16 CEST 2012
On 5/19/12 6:15 AM, Anirban wrote:
> On Sat, May 19, 2012 at 3:21 PM, Turgay Cakmak <turgaycakmak34 at gmail.com
> <mailto:turgaycakmak34 at gmail.com>> wrote:
> Hi Gromacs users,
> I have a question related to the extension of the simulation.
> I have done 10 ns simulation (several peptides in a box). Now, I want to
> extend it 10ns more.
> * As far as I see from “Justin Lemkul’s Lysozyme in water tutorial”, to
> extend simulation, following should be done.
> grompp -f grompp.mdp -c first10ns.gro –t first10ns.cpt -p
> topol.top -o second10ns.tpr
This is not from my tutorial, so I don't know where you found it. In principle,
it is correct, but it is actually easier to extend a simulation. One only needs
to use grompp when changing output frequencies, ensembles, use of position
> * But, another tutorial says that:
> tpbconv -f traj.trr -s topol.tpr -e ener.edr -o tpxout.tpr
> –until $VALUE
> Where $VALUE = ps (e.g. if you wanted to extend a 2 ns run to
> 5 ns, then $VALUE = 5000)
> This option is fine. You don't need the .trr and .edr files if you supply a
> check-point file (.cpt) with -f option, to extend a simulation.
The checkpoint file is not supplied to tpbconv. I would encourage the OP to
read the following, which explains the extension mechanism:
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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