[gmx-users] grompp - commands

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> 
> Hi
> Here are four commands.
> 
> PART I
> 
> grompp_mpi -np 16 -v -f md.mdp -c 6LYZ-MD.gro -p 6LYZ.top -o 6LYZ-MD55.tpr
> 
> mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-MD55
> 
>   
> 
> 
> PART II
> 
> grompp_mpi -np 16 -v -f md.mdp -c 6LYZ-MD55.gro -p 6LYZ.top -o 
> 6LYZ-MD155.tpr 
> 
> mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-MD155 
> 
> 
> Will the last snapshot of trajectory of the simulation PART I be save as 
> 6LYZ-MD55.gro?
> 

Quite clearly, yes.  Please refer to the documented purpose of "mdrun -deffnm."

> Will the commands in PART II intrigue the simulation starting from the 
> last snapshot of trajectory of PART I , 6LYZ-MD55.gro ?
> 

Again, yes.  If you are looking to continue a previous run, however, you are not 
continuing it properly if you do not supply the .trr and .edr file with -t and 
-e, respectively.  This is assuming, based on the presence of the -np flag, that 
you are using version 3.3.x.

I think you will find it far more effective to run your commands and check the 
relevant input and output (most of which can be done in a text editor or by 
simply listing files in a terminal, or at the most using gmxdump) rather than 
waiting for someone to check your work for you.

-Justin

> 
> 
> Thank you
> 
> Lin
> 

-- 
========================================

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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