[gmx-users] Problem with REST2

Wed Apr 1 20:20:21 CEST 2020

Once you run your processed.top with selected hot atoms (via underscore)
through the plumed script, the new .top files (denoted with numbers) should
have scaled values replaced in the appropriate places.  Compare the charges
for instance on the selected atoms in your original processed.top and the
plumed script output .top files.  If they have been scaled appropriately,
removing the underscore shouldn’t matter.  Disclaimer - I’m new at this too!

On Wednesday, April 1, 2020, Joseph, Benjamin Philipp <
benjamin.joseph at rwth-aachen.de> wrote:

> Dear Daniel,
>
> I thought the underscores in the processed.gro file are necessary in order
> to mark the hot atoms and am not sure if all atoms are recognised as cold
> atoms when deleting the underscores.
>
> Best,
>
> Benjamin
>
> > Am 01.04.2020 um 19:10 schrieb Daniel Burns <dburns at iastate.edu>:
> >
> > I haven't had an error from the underscore myself but I haven't been
> using
> > the Amber force field.  Maybe you could try deleting the underscores on
> the
> > input .top files since the plumed script has already scaled them.  The
> > atomtype might be recognized then.
> >
> >> On Wed, Apr 1, 2020 at 11:25 AM Joseph, Benjamin Philipp <
> >> benjamin.joseph at rwth-aachen.de> wrote:
> >>
> >> 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:
> >>
> >> ––––––––––––––––––––
> >> 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
> >> _
> >> ––––––––––––––––––––
> >> The script I use to generate the topol and tpr files is the following:
> >> ––––––––––––––––––––
> >> #!/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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