[gmx-users] extention of the simulation

[Justin A. Lemkul]

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 
restraints, etc.

>       * 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:

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4

-Justin

--
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Justin A. Lemkul, Ph.D.
Research Scientist
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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