On 6/2/12 11:23 AM, rama david wrote:
Thank you Justin for quick reply ....
On Sat, Jun 2, 2012 at 8:12 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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)
Extremely Sorry for my carelessness , New mdp files means the same as previous,
with same number of steps, but just change in output frequency
So as per your recommendation and experience Is any alternative to do these
from 20 ns???
You'll get a mismatch in your files (checkpoint, trajectory, energy) in terms of
frame interval. You should not try to append to these files or extend the run.
Just run a new simulation from 20 -> 30 ns. The grompp command was correct,
assuming you set "tinit = 20000" in the .mdp file and setting nsteps
appropriately to give another 10 ns. Then run it as a new simulation. It will
still be an extension of the first simulation (since the .cpt preserves the
previous state), but without the mdrun -cpi -append mechanism, which in this
case you don't want (or possibly can't use).
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
As per the
link..http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File
I interpreted following things..
1. I have to use the state.cpt , but in the case problem to these I have to use
prev.cpt, I can check there
content by gmxcheck..
But my Query is What are may be the potential problems ?? and how to find
them ??
Crash the run is very often with my system, that why I am worried..
If you're getting frequent crashes, you should investigate why this is happening
rather than just plowing ahead. Are there error messages in the .log or
stdout/stderr output? Are your energetic terms sensible? If the system is
crashing due to physical instability, you're wasting your time producing junk.
If the crashes are occurring due to hardware or filesystem instability, that's
something to take up with your sysadmin.
-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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