From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jun 10 2014 - 02:43:11 CDT
You can simply use a bash script to write multiple namd configs and than call namd for a number of steps that fits your hard disk limit.
Basic example:
#!/bin/bash
for ((i=0; $i<10; $i++))
do
ibefore = $[$i-1]
cat > myconfig_${i}.namd <<ENDIN
if {${1} == 0} {
coordinates my.pdb
temperature 300
} else {
coordinates myconfig_${ibefore}.coor
velocities myconfig_${ibefore}.vel
extendedsystem myconfig_${ibefore}.xsc
}
[your other namd inputs]
outputname myconfig_${i}
run 10000000
ENDIN
namd2 +p4 myconfig_${i}.namd > myconfig_${i}.log 2> myconfig_${i}.e
done
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Shailesh Pandey
Gesendet: Montag, 9. Juni 2014 19:54
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation??
Dear NAMD users,
I am running NAMD simulations, but my problem is that users are allowed to store only limited data (say 100GB) in their account at our computing center, but when i run a simulations of 100ns allocated user space gets filled and simulation is killed by scheduler before completing. I want to simulations of 100ns length because jobs usually wait for weeks in queue only after such long wait get chance to run, So I want when I get chance to run i should run 100ns in one chance.
I want to write different DCD for every (say 20ns) so that once simulation crosses 20 ns, it should start writing to different DCD file and after backing up earlier one I can safely delete older DCD without affecting running simulation.
Eg. setting restartsave yes we can save restart files for every restart timestep, A similar thing i want for DCD file.
I can not increase DCDfreq, because frames are need for analysis.
Any help is appreciated thank you.
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