Many thanks for your answer.
I a bit confuse with the NetCDF trajectory format. If I use this format I will be able to analysis my trajectory with ptraj or even combine trajectory from different run?
Regards,
________________________________________
De : Jason Swails [jason.swails.gmail.com]
Envoyé : vendredi 28 mars 2014 12:48
À : amber.ambermd.org
Objet : Re: [AMBER] Replica exchange restart file
On Fri, 2014-03-28 at 12:15 +0000, Mele N. wrote:
> Dear Amber user,
>
> I running a replica exchange simulation for a peptide in explicit
> water. When the simulation was done I restart it. When I had a look on
> the log file from the second simulation run I realized that the
> simulation did not take care of the target temperature change.
> The target temperature in the second run did not correspond to the
> temperature at the end of the first one.
> For the second run I used the same remd.mdin file and I just change
> the coordinate input file in sander command:
>
> Input file:
>
> Production
> &cntrl
> irest=0, ntx=1,
You need to set irest=1 and ntx=5 if you want sander to actually
restart. With your current settings, sander will ignore any velocities
_and_ temperature that's stored in your restart file (because you told
it to).
> nstlim=1000, dt=0.002,
> ntt=3, gamma_ln=1.0,
> temp0=XXXXX, ig=RANDOM_NUMBER,
If you set ig=-1, the random number is pulled from the wall clock and
basically guaranteed to be different every simulation.
> ntc=2, ntf=2, nscm=1000,
> ntb=1,
> cut=10.0,
> ntpr=100, ntwx=1000, ntwr=100000,
> nmropt=1,
> numexchg=15000,
I **HIGHLY** recommend using ioutfm=1 to write NetCDF trajectories. For
more advanced REMD simulations (i.e., multiple-dimensional REMD) this
will actually become a requirement. But there is almost no advantage to
using ASCII trajectories. They are lower precision, 2 to 5 times
larger, more easily corrupted, and susceptible to overflowing coordinate
positions if iwrap=0 for long simulations (as is true in your input
file).
> /
> &wt TYPE='END'
> /
> DISANG=file.dat
>
>
> Sander command with the previous run rst file:
>
> -A -rem 1 -remlog rem_r2.log -i remd.mdin.001 -o remd_r2.mdout.001 -c remd.rst.001 -r remd_r2.rst.001 -x remd_r2.mdcrd.001 -inf remd_r2.mdinfo.001 -p file.prmtop
> ........
> ........
>
> I had a look on Amber manuel and to restart a simulation it's write
> that the temperature change is taken into consideration.
> Did I forget something?
Yes, you need to tell Amber to restart the calculation, as described
above.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 28 2014 - 06:30:03 PDT
