Dear Amber users,
I'm new to Amber and I would like to divide a MD job into several subjobs. So, I intend to invoke sander.MPI (alternatively pmemd) the following way:
sander.MPI -O -i subjob.inp -o subjob_1.out -c subjob_0.rst -p testjob.top -r subjob_1.rst -ref subjob_0.rst -x subjob_1.mdcrd -inf subjob_1.inf
sander.MPI -O -i subjob.inp -o subjob_2.out -c subjob_1.rst -p testjob.top -r subjob_2.rst -ref subjob_1.rst -x subjob_2.mdcrd -inf subjob_2.inf
sander.MPI -O -i subjob.inp -o subjob_3.out -c subjob_2.rst -p testjob.top -r subjob_3.rst -ref subjob_2.rst -x subjob_3.mdcrd -inf subjob_3.inf
In the subjob.inp file I'll be having ntx=5 and irest=1. My questions are as follows:
1. If the simulation has no restraints (ntr=0), then do I even need to specify -c option?
2. If I do (either because the answer to #1 is yes or ntr=1) then shouldn't the coordinates for the -c option be same (say subjob_0.rst) for all 3 subjobs (i.e. above usage is wrong)?
3. Lets say each subjob is 1 ns in length. Would the combination of the 3 trajectories be identical to a single 3 ns job (run with identical options except for nstlim)?
Thank you in advance,
Maal
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 16 2010 - 12:30:04 PDT
