On Fri, Mar 28, 2014 at 7:20 AM, Mele N. <nm10g13.soton.ac.uk> wrote:
>
> 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?
>
In fact, it will be much faster to process NetCDF trajectories,
particularly if you use cpptraj.
-Dan
>
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Mar 28 2014 - 08:00:02 PDT
