On 5/19/12 6:15 AM, Anirban wrote:
On Sat, May 19, 2012 at 3:21 PM, Turgay Cakmak <[email protected]
<mailto:[email protected]>> 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
--
=======================================
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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