Hi Dan and all,
I use the Amber 10. Yes, the temperature is read from the restart file.
Another question is how to let the recorded running step in mdcrd file
and the acceptance rate in rem.log file follow the previous running.
when I restart my remd simulation, I found the running step is written
from 0 and the acceptance rate is written from 0.0. They don't follow
the previous running records.
Thanks!
Dongshan
On Fri, Jun 4, 2010 at 8:01 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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 Wed Jun 09 2010 - 23:30:05 PDT
