[gmx-users] Regarding continuation of mdrun

[Justin A. Lemkul]

alkasrivastava at iitb.ac.in 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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-- 
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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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