On 6/2/12 10:27 AM, rama david wrote:
Hi Gromacs Friends,
I run a Production run with saving the co-ordinates and velocity
after every 500 steps for 20ns..
Now I want to extend the run but with saving the co-ordinates and velocity
after every 1000 steps for next 30ns (total 50ns)
To perform these task I am using following command
1. grompp -f <New mdp file just change in saving output> -t <.cpt> -c <.gro
file(gro file from position restrained run )> -o new.tpr
2. tpbconv -s new.tpr -0 extend.tpr -extend 30000
3. mdrun -v -deffnm extend -cpi <.cpt> -append
Is these approach is correct??
No. The new.tpr file contains instructions to run from 20 -> 30 ns. There is
no need to then invoke tpbconv. You would also need a new invocation of mdrun,
since the output frequencies won't match. You don't want to append those files
with mdrun (nor will the checkpoint file likely let you).
Second query;
To rerun the crash run, users give .cpt file as input to -mdrun,
My query is, There are two cpt file a) pre.cpt b) .cpt ,
So which one has to given as input???
Use gmxcheck to understand the contents of each. The timestamp will also tell
you a difference, as will reading mdrun -h for an explanation of what the -cpt
option is doing.
-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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