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When patching GROMACS with PLUMED, it is also possible to perform Hamiltonian replica exchange with different topologies. Although this feature is provided together with PLUMED, it is actually a new feature for GROMACS itself that can be enabled using the -hrex flag of mdrun. This implementation is very close to the one used to produce the data in this paper [24]. In case you find it useful, please cite this paper.
In this short tutorial you will learn how to do two things:
plumed partial_tempering. This is actually not directly related to the -hrex flag.Plumed comes with a partial_tempering command line tool that can be used to generate scaled topologies. Notice that you might want to generate these topologies by yourself. This step is totally independent from the use of the -hrex flag.
The partial_tempering tool can be invoked as follows:
plumed partial_tempering scale < processed.top
where scale is the Hamiltonian scaling factor and processed.top is a post-processed topology file (i.e. produced with grompp -pp) where each "hot" atom has a "_" appended to the atom type, e.g. change this
1 HC 1 ACE HH31 1 0.1123 1.008 ; qtot 0.1123
to this:
1 HC_ 1 ACE HH31 1 0.1123 1.008 ; qtot 0.1123
Notice that the section that should be edited is the [atoms] section for all the molecules that you wish to affect (typically only for the solute, but you may also want to change solvent parameters). If you select all the atoms of the solute, you will be able to prepare topologies such as those needed in a REST2 simulation [94].
Also remember to first produce the processed.top file with grompp -pp. Editing a normal topol.top file will not work, because it does not contain all the parameters. The processed.top file should not have any "#include" statement.
# produce a processed topology grompp -pp # choose the "hot" atoms vi processed.top # generate the actual topology plumed partial_tempering $scale < processed.top > topol$i.top
Warnings:
Suggested tests:
grompp -o topol-unscaled.tpr grompp -pp vi processed.top # choose the "hot" atoms appending "_". You can choose whatever. plumed partial_tempering 1.0 < processed.top > topol-scaled.top # scale with factor 1 grompp -p topol-scaled.top -o topol-scaled.tpr # Then do a rerun on a trajectory mdrun -s topol-unscaled.tpr -rerun rerun.trr mdrun -s topol-scaled.tpr -rerun rerun.trr # and compare the resuling energy files. they should be identical
If GROMACS has been patched with PLUMED it should accept the -hrex option in mdrun. Please double check this (mdrun -h should list this possibility). Notice that not all the versions of GROMACS allow this feature. First of all prepare separate topologies for each replicas using plumed partial_tempering tool as shown above (or using some other tool). Then run a normal replica exchange with gromacs adding the flag "-hrex" on the command line.
A complete run script could be adapted from the following
# five replicas
nrep=5
# "effective" temperature range
tmin=300
tmax=1000
# build geometric progression
list=$(
awk -v n=$nrep \
-v tmin=$tmin \
-v tmax=$tmax \
'BEGIN{for(i=0;i<n;i++){
t=tmin*exp(i*log(tmax/tmin)/(n-1));
printf(t); if(i<n-1)printf(",");
}
}'
)
# clean directory
rm -fr \#*
rm -fr topol*
for((i=0;i<nrep;i++))
do
# choose lambda as T[0]/T[i]
# remember that high temperature is equivalent to low lambda
lambda=$(echo $list | awk 'BEGIN{FS=",";}{print $1/$'$((i+1))';}')
# process topology
# (if you are curious, try "diff topol0.top topol1.top" to see the changes)
plumed partial_tempering $lambda < processed.top > topol$i.top
# prepare tpr file
# -maxwarn is often needed because box could be charged
grompp_mpi_d -maxwarn 1 -o topol$i.tpr -f grompp$i.mdp -p topol$i.top
done
mpirun -np $nrep gmx_mpi mdrun_d -v -plumed plumed.dat -multi $nrep -replex 100 -nsteps 15000000 -hrex -dlb no
Notice that total cell could be charged. This happens whenever the scaled portion of the system is not neutral. There should be no problem in this. When used with pbc, GROMACS will add a compensating background.
Suggested check:
Notice that when you run with GPUs acceptance could be different from 1.0. The reason is that to compute the acceptance GROMACS is sending the coordinates to the neighboring replicas which then recompute energy. If all the tpr files are identical, one would expect energy to be identically to the originally computed one. However, calculations made with GPUs are typically not reproducible to machine precision. For a large system, even an error in the total energy for the last significant digit could be on the order of a kJ. This results in practice in a lower acceptance. The error induced on the final ensemble is expected to be very small.
Warnings:
-dlb no) otherwise the simulation could crash randomly, see #410.
1.8.14