Chandan Choudhury wrote:
Hi Mark !!!
Thanks for answering.
My query is how do I restart my mdrun because the command
nohup mpirun -np 16 -machinefile mac mdrun -s md5-10.tpr -cpi state.cpt
-append &
will not start from where the trajectory was stopped (i.e; time
9169.500). As this command will continue the simulation from where the
cpt file was written.
Right, it will start from whenever the checkpoint was written. You should also
have a state_prev.cpt that is a backup in case this type of thing happens; it
may help. Regardless, with a 36-GB .trr file, the -append option will not work.
Leave it out and use trjcat later.
-Justin
Any suggestions??
chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Tue, Feb 16, 2010 at 9:36 PM, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
On 17/02/10 02:52, Chandan Choudhury wrote:
Hello gmxusers !!!
I want to continue my simulation, from where the point where it
stopped.
The gmxcheck on .trr and cpt files are as:
$gmxcheck -f state.cpt
Checking file state.cpt
# Atoms 186864
Last frame -1 time 9362.500
Item #frames Timestep (ps)
Step 1
Time 1
Lambda 1
Coords 1
Velocities 1
Forces 0
Box 1
$gmxcheck -f 5-10.trr
Checking file 5-10.trr
trn version: GMX_trn_file (single precision)
Reading frame 0 time 5169.500
# Atoms 186864
Reading frame 8000 time 9169.500
Item #frames Timestep (ps)
Step 8395 0.5
Time 8395 0.5
Lambda 8395 0.5
Coords 8395 0.5
Velocities 8395 0.5
Forces 0
Box 8395 0.5
There is a mismatch of time in both the outputs.
The date of modification of both the files as shown are:
Feb 15 19:55 state.cpt
$date -r 5-10.trr
Mon Feb 15 19:59:56 IST 2010
The cpt file shows time greater than the trr file. But the time of
modification of cpt file is less than trr file.
If the simulation stopped catastrophically, then the timestamp could
easily differ, especially if the .cpt is opened, written to and
closed periodically, and the .trr is open continuously.
Cannot understand the,
how to restart the mdrun. And the size of the trr file is 36GB.
Can I
use the append flag in mdrun for gmx 4.0.5.
Search the webpage for suggestions.
Mark
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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