[gmx-users] Problem with REST2

Wed Apr 1 20:22:43 CEST 2020

Okay, now I understand what you mean. Then I should try deleting the underscores in the created top files. This really startled me though, because I never had this problem in the past. Thanks for your help!

Best,

Benjamin

> Am 01.04.2020 um 20:20 schrieb Daniel Burns <dburns at iastate.edu>:
> 
> 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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