Sai Pooja wrote:
I would be happy to supply more information.. if someone could please
look into this.. otherwise I will have to switch to storing every file
and then just concatenating them which seems like a rather roundabout
way of doing it.
In theory, there's nothing wrong with what you've done. What version of Gromacs
is this? Are there any error messages written to the .log file or stdout? In
general, when something goes wrong, Gromacs is fairly vocal about it.
-Justin
On Fri, Jan 28, 2011 at 4:37 PM, Sai Pooja <saipo...@gmail.com
<mailto:saipo...@gmail.com>> wrote:
This is the command:
nbs submit -command "(/usr/local/gromacs/4.5.1/bin/mdrun_mpi -s
rex_3.tpr -e rex_3 -c after_rex_3 -cpi restart3 -cpo restart3 -ap
pend -g rexlog3 -x rextraj3);" -nproc 1 -name "GENHAM-DIHEDRAL-3"
-mail start end
Pooja
On Fri, Jan 28, 2011 at 4:20 PM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote:
On 29/01/2011 3:56 AM, Sai Pooja wrote:
Hi,
I am using tpbconv and mdrun to extend a simulation. I use
it with the append option but the files still get
overwritten or erased. Can someone help me in this regard?
Pooja
Commands (in python)
cmd = '(%s/tpbconv -extend %f -s rex_%d.tpr -o rex_%d.tpr)'
%(GROMPATH,dtstep,i,i)
os.system(cmd)
time.sleep(1)
cmd = 'nbs submit -command "'
cmd += '(%s/mdrun_mpi -noh -noversion -s rex_%d.tpr -e
rex_%d -c after_rex_%d -cpi restart%d -cpo restart%d -append
-g rexlog%d -x rextraj%d >/dev/null); '
%(GROMPATH,i,i,i,i,i,i,i)
cmd += '" '
cmd += '-nproc 1 '
cmd += '-name "GENHAM-DIHEDRAL-%d" '%(i)
cmd += '-mail start end '
cmd += '-elapsed_limit 16h >> rexid'
os.system(cmd)
More useful for diagnostic and record-preservation purposes is
to construct the cmd string and print it to stdout (or something).
At the moment it is far from clear that your -cpi file exists
for the new run.
Mark
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Quaerendo Invenietis-Seek and you shall discover.
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Quaerendo Invenietis-Seek and you shall discover.
--
========================================
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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