Dear members of the gromacs mailing list,
I have problems setting up REST2 (replica exchange with solute tempering)
calculations. The version of PLUMED with GROMACS I use is GROMACS/2018.3-plumed
and the forcefield I am using is amber14sb_parmbsc1.ff. The error occurs when I
try to set up the different topol.top files for the different replicas after
having performed the minimisation, simulated annealing, NVT, NPT and 100 ns
production MD. I get the following error message:
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GROMACS: gmx grompp, version 2018.3
Executable:
/usr/local/software/jureca/Stages/Devel-2018b/software/GROMACS/2018.3-intel-para-2018b-plumed/bin/gmx_mpi
Data prefix:
/usr/local/software/jureca/Stages/Devel-2018b/software/GROMACS/2018.3-intel-para-2018b-plumed
Working dir: /p/scratch/cias-5/joseph1/new/S_1/sys1/neu
Command line:
gmx_mpi grompp -maxwarn 2 -o topol1.tpr -c sa.gro -f md.mdp -p topol1.top
Ignoring obsolete mdp entry 'title'
Setting the LD random seed to -1452668066
WARNING 1 [file topol1.top, line 95]:
Too few parameters on line (source file
/dev/shm/swmanage/GROMACS/2018.3/intel-para-2018b-plumed/gromacs-2018.3/src/gromacs/gmxpreprocess/toppush.cpp,
line 345)
WARNING 2 [file topol1.top, line 97]:
Too few parameters on line (source file
/dev/shm/swmanage/GROMACS/2018.3/intel-para-2018b-plumed/gromacs-2018.3/src/gromacs/gmxpreprocess/toppush.cpp,
line 345)
Generated 14878 of the 14878 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 14878 of the 14878 1-4 parameter combinations
ERROR 1 [file topol1.top, line 1813]:
Atomtype 3C_ not found
_
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The script I use to generate the topol and tpr files is the following:
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#!/bin/bash
#16 replicas
nrep=16
# "effective" temperature range
tmin=287
tmax=400
# 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
gmx_mpi grompp -maxwarn 2 -o topol$i.tpr -c md.gro -f md.mdp -p topol$i.top
done
––––––––––––––––––––
I think that the problem might be that PLUMED does not support the force field
I am using. Using AMBER99SB-ILDN, nucleic AMBER 94 I did not have these issues
(using the same script). Do you have any suggestions what could be the problem
here? Thanks a lot!
Best,
Benjamin Joseph
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