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 <[email protected]>: > > 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 < >> [email protected]> 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 <[email protected]>: >>> >>> 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 < >>>> [email protected]> 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 >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to [email protected]. >>>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to [email protected]. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to [email protected]. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
