[AMBER] How to restart the remd simulation following the remd tutorial?

From: Dongshan Wei <dswei0523.gmail.com>
Date: Thu, 3 Jun 2010 16:29:43 -0400

Hi All,

I followed the remd tutorial to do a short remd simulation and now I
want to restart the remd to do a long production simulation. Now I
have the following servral questions:

(1) If I want to append all of the output, should I replace the -O
with -A in remd.groupfile or add -A in the command line "mpirun -np 8
sander.MPI -ng groupfile remd.groupfile"?

(2) What is the restart mdin script and how to let the new extented
remd to read the target temperature from restart .incprd file not from
the remd.mdin file? I try to use the following script (I did the
explicit remd, so I cancelled the restrain and nmr commands):

   irest=1, ntx=7,
   nstlim=100, dt=0.002,
   ntt=3, gamma_ln=1.0,
   ntc=2, ntf=2, nscm=1000,
   cut = 10.0, ntr = 0,
   ntpr=1000, ntwx=1000, ntwr=10000,

The remd.groupfile looks like:

-A -rem 1 -remlog rem.log -i remd.mdin.001 -o remd.mdout.001 -c
remd.rst.001 -r remd.rst2ns.001 -x remd.mdcrd.001 -inf remd.mdinfo.001
-p ala10_wat.prmtop
-A -rem 1 -remlog rem.log -i remd.mdin.002 -o remd.mdout.002 -c
remd.rst.002 -r remd.rst2ns.002 -x remd.mdcrd.002 -inf remd.mdinfo.002
-p ala10_wat.prmtop

When I used the above remd.mdin and remd.groupfile, I observed the new
remd override the output and doesn't read the correct target

Could you point out my problems or send me the remd restart files
(remd.mdin and setup_remd_input.x )?

Thanks a lot.


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Received on Thu Jun 03 2010 - 14:00:03 PDT
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