What version of Amber are you using? In recent versions of Amber (10
and 11) during REMD runs the temperature is read from the restart file
if present and irest=1.
Also, this is just my opinion but I would recommend against appending
your output from separate runs. If anything goes wrong it will be a
lot harder for you to track down what happened.
-Dan
On Thu, Jun 3, 2010 at 4:29 PM, Dongshan Wei <dswei0523.gmail.com> wrote:
> 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):
>
> remd
> &cntrl
> irest=1, ntx=7,
> nstlim=100, dt=0.002,
> ntt=3, gamma_ln=1.0,
> temp0=XXXXX, ig=RANDOM_NUMBER,
> ntc=2, ntf=2, nscm=1000,
> ntb=1,
> cut = 10.0, ntr = 0,
> ntpr=1000, ntwx=1000, ntwr=10000,
> numexchg=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
> temperature.
>
> Could you point out my problems or send me the remd restart files
> (remd.mdin and setup_remd_input.x )?
>
> Thanks a lot.
>
> Dongshan
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
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Received on Fri Jun 04 2010 - 05:30:03 PDT
