[email protected] wrote:
Hello everyone
I have a doubt regarding the extension of simulation in newer version of
gromacs (4.0.4).
1)
If simulation has completed and one wants to extend it further the option
used is
tpbconv -s full_part3.tpr -extend timetoextendby -o full_part4.tpr
and then mdrun as usual with an additional flag for cpt file like this
nohup mpirun -np 4 mdrun_mpi_d -v -s full_part4.tpr -c full_part4.gro -o
full_part4.trr -x full_part4.xtc -e full_part4.edr -g full_part4.log -cpi
state.cpt >& full_part4.job &
After this what i am getting is that it is changing the files names as :
full_part4.trr to full_part4.part0002.trr
Is is normal?
Yes. To turn it off, use mdrun -noaddpart.
2) My another doubt is that whether I have to give cpt file in tpbconv as
well?
No.
<snip>
3)If the simulation has been crashed then there is no need to make the tpr
file only the mdrun with cpt file and append option is all that required
like this
nohup mpirun -np 4 mdrun_mpi_d -v -s full_part3.tpr -c full_part3.gro -o
full_part3.trr -x full_part3.xtc -e full_part3.edr -g full_part3.log -cpi
state.cpt >& full_part3.job &
Is it correct?
Yes. To make your life easier, use the -deffnm option of mdrun; saves a lot of
repetitive typing :)
-Justin
Could anyone please clear my doubts.
Thanks in advance
Alka
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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