Hi Raimon,
Reservoir REMD is currently implemented only in Sander (it will be in pmemd
soon). The easiest way to build a reservoir is by using the cpptraj command
"createreservoir".
cpptraj <<EOF
parm topology.top
trajin trajectory.nc
readdata energies.dat name energy
createreservoir reservoir.nc ene energy iseed 1 temp0 363.3
EOF
"topology.top" is the topology of the structures you are loading.
"trajectory.nc" contains all the structures that you want to use in the
reservoir in NetCDF format.
"energies.dat" is a single-column file with energies for each corresponding
structure in trajectory.nc, we store these values in a cpptraj dataset
named "energy".
"createreservoir" will create the NetCDF reservoir file "reservoir.nc" that
has the structures and their corresponding energies. "temp0" is the
temperature of the reservoir. "iseed" is the random seed generator for
picking reservoir structures. "trajectory.nc" can have velocities
corresponding to each structure too but it is not mandatory.
Once cpptraj creates "reservoir.nc", there is one more step to do. The
"temp0" field in reservoir NetCDF files has to renamed to remd_values. The
following set of commands do this.
ncdump reservoir.nc >temp.dat; sed -I 's/temp0/remd_values/' temp.dat;
ncgen -o newreservoir.nc -x temp.dat
You can check temp.dat to see if all your structures and energies are
loaded correctly.
Once you have "reservoir.nc", using it is quite easy. The groupfile is
similar to REMD but with 2 additions. Instead of it being
-rem 1 remlog rem.log ….
It will be
-rem 1 -rremd 1 -reservoir newreservoir.nc remlog rem.log
Note that rremd=1 corresponds to Boltzmann reservoir REMD and rremd=2
corresponds to Non-Boltzmann reservoir REMD.
Let me know if you have any issues.
Best,
Koushik
On Tue, Mar 19, 2019 at 4:17 AM Raimon Fabregat <raimon.fabregat.epfl.ch>
wrote:
> Dear all,
>
> I have a working standard REMD simulation, and I want to replace the
> highest temperature by a 'reservoir'. I have followed the instructions
> in the AMBER manual, but I haven't been able to understand how the input
> files should be modified. Has any of you some working input files that I
> could use as a guide?
>
> Thanks a lot for your help.
>
> Best,
>
> Raimon
>
>
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Received on Tue Mar 19 2019 - 03:00:02 PDT
