[gmx-users] Atom CA used in that entry is not found in the input file
Hello, I edited a few selenomethionine residues, changing "S" to "SD" and removed the "SE" at the end of the line. I then ran pdb2gmx with Charmm36. I get the following error (not sure why the residue number doesn't match): Fatal error: Residue 324 named GLY of a molecule in the input file was mapped to an entry in the topology database, but the atom CA used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. My .pdb file section looks like this: ATOM569 N MET A 324 87.364 46.446 53.851 1.00 3.42 N ATOM570 CA MET A 324 86.617 45.972 52.679 1.00 6.50 C ATOM571 C MET A 324 87.405 46.212 51.424 1.00 6.43 C ATOM572 O MET A 324 86.987 45.830 50.332 1.00 8.80 O ATOM573 CB MET A 324 85.203 46.573 52.584 1.00 5.66 C ATOM574 CG MET A 324 84.258 46.053 53.663 1.00 5.50 C ATOM575 CE MET A 324 83.200 44.225 51.772 1.00 3.19 C ATOM576 SD MET A 324 83.876 44.132 53.563 1.00 14.27 S ATOM577 N GLY A 325 88.553 46.854 51.604 1.00 9.51 N ATOM578 CA GLY A 325 89.548 47.012 50.546 1.00 9.78 C ATOM579 C GLY A 325 89.087 47.608 49.227 1.00 9.91 C ATOM580 O GLY A 325 89.352 47.048 48.159 1.00 11.43 O ATOM581 N GLY A 326 88.403 48.742 49.271 1.00 7.35 N ATOM582 CA GLY A 326 87.942 49.290 48.005 1.00 6.34 C ATOM583 C GLY A 326 86.542 48.875 47.602 1.00 3.91 C ATOM584 O GLY A 326 85.947 49.547 46.765 1.00 4.00 O I don't see anything wrong with my GLY residues and none of the other Glycines are presenting an error. This does follow one of my edited MET residues. Thank you, Dan -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] restarting a simulation
You should also have an "md10.cpt" in addition to the "md10_prev.cpt"? If so, replace it in your command with just the md10.cpt file. If you don't have it, try renaming your "_prev.cpt" file to just "md10.cpt". Dan On Mon, Apr 6, 2020 at 11:06 AM Sadaf Rani wrote: > Dear Gromacs users > I am restarting a simulation with the following command:- > mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append > > However, I am getting following error message. All the below-named files > are there in my directory but it still complains the same. > > Inconsistency in user input: > Some output files listed in the checkpoint file md10_prev.cpt are not > present > or not named as the output files by the current program:)Expected output > files > that are present: > > Expected output files that are not present or named differently: > md10.log > md10.xtc > md10.trr > md10.edr > md10.xvg > To keep your simulation files safe, this simulation will not restart. > Either > name your > output files exactly the same as the previous simulation part (e.g. with > -deffnm), or > make sure all the output files are present (e.g. run from the same > directory > as the > previous simulation part), or instruct mdrun to write new output files with > mdrun -noappend. > In the last case, you will not be able to use appending in future for this > simulation. > > I also tried without -append option. > Please correct me if I am wrong somewhere. > Thanks. > > Sadaf > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
Start here: http://www.mdtutorials.com/gmx/. An introduction to linux book might be helpful as well if you are not already familiar with it. Good luck! On Thu, Apr 2, 2020 at 2:05 PM Feriel Terbeche wrote: > Hello! > My name's FERIEL TERBECHE I am a genetic studant, from ALGERIA, Im > preparing my last study's project (master degrees), wich is about > hemophila A and factor VIII where I have to use gromacs, but, I don't know > how to use it even I have it on my computer and unfortunately no one here > can help me because no one used it before. I really need help but I don't > know from where I'll get it, so can I have some advices. Thank you > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem with REST2
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.jos...@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 :
> >
> > 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.jos...@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 >>t=tmin*exp(i*log(tmax/tmin)/(n-1));
> >>printf(t); if(i >> }
> >> }'
> >> )
> >>
> >> # clean directory
> >> rm -fr \#*
> >> rm -fr topol*
> >>
> >> for((i=0;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_mp
Re: [gmx-users] Problem with REST2
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.jos...@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 t=tmin*exp(i*log(tmax/tmin)/(n-1));
> printf(t); if(i }
> }'
> )
>
> # clean directory
> rm -fr \#*
> rm -fr topol*
>
> for((i=0;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 gmx-users-requ...@gromacs.org.
>
--
Gromacs Users mailing list
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Re: [gmx-users] Replica exchange: Coordinates and simulation box size?
Hi Johannes, Somebody please correct me if I'm wrong but I believe it is just the thermostats that are exchanged. A given simulation box's velocities are rescaled accordingly after the exchange and the simulation continues with its own fluctuations in box size assuming it is pressure-coupled. I don't know anything about incorporating free energy calculations with replica exchange though. Aloha, Dan On Mon, Mar 23, 2020 at 11:07 AM Johannes Hermann wrote: > Dear all, > > I have slightly different Position Restrains and Box sizes over my > lambda windows in an alchemical Free Energy Calculation in NVT ensemble > (I know that my calculated Free Energy Difference will not solely depend > on the mutation alone..) > > What happens if I use replica exchange? What exactly is exchanged within > different windows: Only the coordinates or also the current simulation > box size? > > Thanks in advance! > > All the best > > Johannes > > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] checkpoint files with replica exchange/ -multidir
I started another run to check exchanges after letting the systems equilibrate more. I made the input by using grompp with the .cpt file - now they are exchanging 100% of the time. Each file was grompped with it's own original tpr and cpt file - I can't figure out what's happening. Dan On Thu, Mar 12, 2020 at 2:49 PM Daniel Burns wrote: > Thanks Mark, > > From my experience so far if I stayed at 4ps, I would continue to get > lower exchange rates. > > As for starting at 1ps, my system must not have been equilibrated because > it was blowing up on the first exchange attempt which Is why I decided to > restart with the checkpoint file. > > Dan > > On Thu, Mar 12, 2020 at 2:44 PM Mark Abraham > wrote: > >> Hi, >> >> On Thu, 12 Mar 2020 at 20:39, Daniel Burns wrote: >> >> > Hello, >> > >> > I'm using 2 replicas to test exchange conditions. I restarted a run and >> > included the checkpoint file name (which is identical in each directory >> > provided under the -multidir option). After the restart, I'm getting >> 100% >> > exchange when before it was 50%. >> > >> > Does the -cpi option work properly for replica exchange/ multidir runs? >> > >> >> As far as we know :-) >> >> The only thing I changed was the exchange attempt frequency from every 4ps >> > to 1ps. >> > >> >> What happens if you start at 4 and stay there? Start at 1 and stay there? >> >> Mark >> >> >> > Thank you, >> > >> > Dan >> > -- >> > 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 gmx-users-requ...@gromacs.org. >> > >> -- >> 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 gmx-users-requ...@gromacs.org. >> > -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] checkpoint files with replica exchange/ -multidir
Thanks Mark, >From my experience so far if I stayed at 4ps, I would continue to get lower exchange rates. As for starting at 1ps, my system must not have been equilibrated because it was blowing up on the first exchange attempt which Is why I decided to restart with the checkpoint file. Dan On Thu, Mar 12, 2020 at 2:44 PM Mark Abraham wrote: > Hi, > > On Thu, 12 Mar 2020 at 20:39, Daniel Burns wrote: > > > Hello, > > > > I'm using 2 replicas to test exchange conditions. I restarted a run and > > included the checkpoint file name (which is identical in each directory > > provided under the -multidir option). After the restart, I'm getting > 100% > > exchange when before it was 50%. > > > > Does the -cpi option work properly for replica exchange/ multidir runs? > > > > As far as we know :-) > > The only thing I changed was the exchange attempt frequency from every 4ps > > to 1ps. > > > > What happens if you start at 4 and stay there? Start at 1 and stay there? > > Mark > > > > Thank you, > > > > Dan > > -- > > 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 gmx-users-requ...@gromacs.org. > > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
[gmx-users] checkpoint files with replica exchange/ -multidir
Hello, I'm using 2 replicas to test exchange conditions. I restarted a run and included the checkpoint file name (which is identical in each directory provided under the -multidir option). After the restart, I'm getting 100% exchange when before it was 50%. Does the -cpi option work properly for replica exchange/ multidir runs? The only thing I changed was the exchange attempt frequency from every 4ps to 1ps. Thank you, Dan -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding REMD using gromacs4.5.5
Hi Amit, I’m not the best resource for solutions but I’ve been having this issue with gromacs 2018. It seems to be related to the process manager or our open mpi module we are using. The job would hang on some open mpi communication step. I found it would work if each replica was assigned its own entire node but that becomes prohibitively resource expensive with more than a few replicas. I was finally able to get it to work on our least used cluster where things must have been installed correctly. You might have your IT look at what’s happening with the process manager and open mpi or whatever dependencies you have loaded. You might try a small job where you can assign each replica to its own node and see if you get the full output. Our IT dept has been working for two weeks and still haven’t gotten it to work on the other clusters. Dan On Tuesday, March 3, 2020, Amit Kumar wrote: > Dear Gromacs users, > > I am trying to run a REMD simulation in gromacs 4.5.5 in implicit solvent > but I am unable to get any output file containing significant data (logfile > is obtained with only developers' details) or any error file. > I am unable to understand why this is happening and how can I tackle the > situation? > Kindly, help me out of this situation. > > ThankYou > Amit Kumar > -- 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 gmx-users-requ...@gromacs.org.
[gmx-users] replica exchange 1%
Hi, I'm using the Plumed plugin to perform a "Hamiltonian" replica exchange. I have histograms of the total energies of each system that share a huge overlap - on the order of 80%. Only a small subset of the residues have perturbed energy functions. Replica exchange attempts only happen every 2000 steps. Pressure coupling is every 5 steps. Despite the above, I am only experiencing successful exchanges 1% of the time. Any suggestions on what might be the reason for such low exchange probabilities? Thank you! Dan -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD stall out
This was not actually the solution. Wanted to follow up in case someone else is experiencing this problem. We are reinstalling the openmp version. On Thu, Feb 20, 2020 at 3:10 PM Daniel Burns wrote: > Hi again, > > It seems including our openmp module was responsible for the issue the > whole time. When I submit the job only loading pmix and gromacs, replica > exchange proceeds. > > Thank you, > > Dan > > On Mon, Feb 17, 2020 at 9:09 AM Mark Abraham > wrote: > >> Hi, >> >> That could be caused by configuration of the parallel file system or MPI >> on >> your cluster. If only one file descriptor is available per node to an MPI >> job, then your symptoms are explained. Some kinds of compute jobs follow >> such a model, so maybe someone optimized something for that. >> >> Mark >> >> On Mon, 17 Feb 2020 at 15:56, Daniel Burns wrote: >> >> > HI Szilard, >> > >> > I've deleted all my output but all the writing to the log and console >> stops >> > around the step noting the domain decomposition (or other preliminary >> > task). It is the same with or without Plumed - the TREMD with Gromacs >> only >> > was the first thing to present this issue. >> > >> > I've discovered that if each replica is assigned its own node, the >> > simulations proceed. If I try to run several replicas on each node >> > (divided evenly), the simulations stall out before any trajectories get >> > written. >> > >> > I have tried many different -np and -ntomp options as well as several >> slurm >> > job submission scripts with node/ thread configurations but multiple >> > simulations per node will not work. I need to be able to run several >> > replicas on the same node to get enough data since it's hard to get more >> > than 8 nodes (and as a result, replicas). >> > >> > Thanks for your reply. >> > >> > -Dan >> > >> > On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns >> wrote: >> > >> > > Hi, >> > > >> > > I continue to have trouble getting an REMD job to run. It never >> makes it >> > > to the point that it generates trajectory files but it never gives any >> > > error either. >> > > >> > > I have switched from a large TREMD with 72 replicas to the Plumed >> > > Hamiltonian method with only 6 replicas. Everything is now on one >> node >> > and >> > > each replica has 6 cores. I've turned off the dynamic load balancing >> on >> > > this attempt per the recommendation from the Plumed site. >> > > >> > > Any ideas on how to troubleshoot? >> > > >> > > Thank you, >> > > >> > > Dan >> > > >> > -- >> > 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 gmx-users-requ...@gromacs.org. >> > >> -- >> 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 gmx-users-requ...@gromacs.org. >> > -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD stall out
Hi again, It seems including our openmp module was responsible for the issue the whole time. When I submit the job only loading pmix and gromacs, replica exchange proceeds. Thank you, Dan On Mon, Feb 17, 2020 at 9:09 AM Mark Abraham wrote: > Hi, > > That could be caused by configuration of the parallel file system or MPI on > your cluster. If only one file descriptor is available per node to an MPI > job, then your symptoms are explained. Some kinds of compute jobs follow > such a model, so maybe someone optimized something for that. > > Mark > > On Mon, 17 Feb 2020 at 15:56, Daniel Burns wrote: > > > HI Szilard, > > > > I've deleted all my output but all the writing to the log and console > stops > > around the step noting the domain decomposition (or other preliminary > > task). It is the same with or without Plumed - the TREMD with Gromacs > only > > was the first thing to present this issue. > > > > I've discovered that if each replica is assigned its own node, the > > simulations proceed. If I try to run several replicas on each node > > (divided evenly), the simulations stall out before any trajectories get > > written. > > > > I have tried many different -np and -ntomp options as well as several > slurm > > job submission scripts with node/ thread configurations but multiple > > simulations per node will not work. I need to be able to run several > > replicas on the same node to get enough data since it's hard to get more > > than 8 nodes (and as a result, replicas). > > > > Thanks for your reply. > > > > -Dan > > > > On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns > wrote: > > > > > Hi, > > > > > > I continue to have trouble getting an REMD job to run. It never makes > it > > > to the point that it generates trajectory files but it never gives any > > > error either. > > > > > > I have switched from a large TREMD with 72 replicas to the Plumed > > > Hamiltonian method with only 6 replicas. Everything is now on one node > > and > > > each replica has 6 cores. I've turned off the dynamic load balancing > on > > > this attempt per the recommendation from the Plumed site. > > > > > > Any ideas on how to troubleshoot? > > > > > > Thank you, > > > > > > Dan > > > > > -- > > 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 gmx-users-requ...@gromacs.org. > > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD stall out
Thanks Mark and Szilard, I forwarded Mark's suggestion to IT. I'll see what they have to say and then I'll try the simulation again and open an issue on redime. Thank you, Dan On Mon, Feb 17, 2020 at 9:09 AM Mark Abraham wrote: > Hi, > > That could be caused by configuration of the parallel file system or MPI on > your cluster. If only one file descriptor is available per node to an MPI > job, then your symptoms are explained. Some kinds of compute jobs follow > such a model, so maybe someone optimized something for that. > > Mark > > On Mon, 17 Feb 2020 at 15:56, Daniel Burns wrote: > > > HI Szilard, > > > > I've deleted all my output but all the writing to the log and console > stops > > around the step noting the domain decomposition (or other preliminary > > task). It is the same with or without Plumed - the TREMD with Gromacs > only > > was the first thing to present this issue. > > > > I've discovered that if each replica is assigned its own node, the > > simulations proceed. If I try to run several replicas on each node > > (divided evenly), the simulations stall out before any trajectories get > > written. > > > > I have tried many different -np and -ntomp options as well as several > slurm > > job submission scripts with node/ thread configurations but multiple > > simulations per node will not work. I need to be able to run several > > replicas on the same node to get enough data since it's hard to get more > > than 8 nodes (and as a result, replicas). > > > > Thanks for your reply. > > > > -Dan > > > > On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns > wrote: > > > > > Hi, > > > > > > I continue to have trouble getting an REMD job to run. It never makes > it > > > to the point that it generates trajectory files but it never gives any > > > error either. > > > > > > I have switched from a large TREMD with 72 replicas to the Plumed > > > Hamiltonian method with only 6 replicas. Everything is now on one node > > and > > > each replica has 6 cores. I've turned off the dynamic load balancing > on > > > this attempt per the recommendation from the Plumed site. > > > > > > Any ideas on how to troubleshoot? > > > > > > Thank you, > > > > > > Dan > > > > > -- > > 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 gmx-users-requ...@gromacs.org. > > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD stall out
HI Szilard, I've deleted all my output but all the writing to the log and console stops around the step noting the domain decomposition (or other preliminary task). It is the same with or without Plumed - the TREMD with Gromacs only was the first thing to present this issue. I've discovered that if each replica is assigned its own node, the simulations proceed. If I try to run several replicas on each node (divided evenly), the simulations stall out before any trajectories get written. I have tried many different -np and -ntomp options as well as several slurm job submission scripts with node/ thread configurations but multiple simulations per node will not work. I need to be able to run several replicas on the same node to get enough data since it's hard to get more than 8 nodes (and as a result, replicas). Thanks for your reply. -Dan On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns wrote: > Hi, > > I continue to have trouble getting an REMD job to run. It never makes it > to the point that it generates trajectory files but it never gives any > error either. > > I have switched from a large TREMD with 72 replicas to the Plumed > Hamiltonian method with only 6 replicas. Everything is now on one node and > each replica has 6 cores. I've turned off the dynamic load balancing on > this attempt per the recommendation from the Plumed site. > > Any ideas on how to troubleshoot? > > Thank you, > > Dan > -- 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 gmx-users-requ...@gromacs.org.
[gmx-users] REMD stall out
Hi, I continue to have trouble getting an REMD job to run. It never makes it to the point that it generates trajectory files but it never gives any error either. I have switched from a large TREMD with 72 replicas to the Plumed Hamiltonian method with only 6 replicas. Everything is now on one node and each replica has 6 cores. I've turned off the dynamic load balancing on this attempt per the recommendation from the Plumed site. Any ideas on how to troubleshoot? Thank you, Dan -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy plots for specific atoms/selections
Thanks, Justin. I wanted to confirm that the plumed scaled topology function is working properly on the selected atoms but maybe this isn't the right way. I've already confirmed that the system's total energy is different between a scaled and unscaled system but the tutorial makes it sounds as if you can expect a precise value based on your scaling factor if you plot the energies for just the scaled atoms. Thanks again! Dan On Wed, Feb 5, 2020 at 6:10 AM Justin Lemkul wrote: > > > On 1/31/20 6:23 PM, Daniel Burns wrote: > > Hi, > > > > I want to get an xvg file that will show me the LJ, Coulomb, and dihedral > > energies on a specific set of atoms. I've tried passing a .dat file with > > the groups of atoms from gmx select to gmx enemat but I get an error > > message saying that I must not have included those groups in my mdp file. > > How do I incorporate them into my mdp file if I don't want specific mdp > > options to work on them? > > > > I cannot figure out how to retrieve the data on my groups of interest. > I've > > tried -rerun and included an index of the atoms of interest as well > > > > If anybody has a detailed explanation, I would be grateful. > > Create an index file that defines the atoms of interest, create a > matching trajectory with trjconv and new .tpr file with only those atoms > using convert-tpr, then use mdrun -rerun with those new files. Be > advised that simply chopping out atoms and computing energies like this > is unlikely to have any physical meaning. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
[gmx-users] Energy plots for specific atoms/selections
Hi, I want to get an xvg file that will show me the LJ, Coulomb, and dihedral energies on a specific set of atoms. I've tried passing a .dat file with the groups of atoms from gmx select to gmx enemat but I get an error message saying that I must not have included those groups in my mdp file. How do I incorporate them into my mdp file if I don't want specific mdp options to work on them? I cannot figure out how to retrieve the data on my groups of interest. I've tried -rerun and included an index of the atoms of interest as well If anybody has a detailed explanation, I would be grateful. Thank you, Dan -- 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 gmx-users-requ...@gromacs.org.
[gmx-users] T-REMD stalled - no trr files generated
Hi, I have a system containing a dimer totaling about 600 residues solvated with 32,000 water molecules. I have 72 replicas that are spread between 300 - 406 K. Each replica is running on 5 Intel Skylake 6140 cores. The simulations have been running for 14 hours and no trr files have been generated and the md logs have not moved past the "maximum allowed distance for charge groups involved in interactions" section. I have run quick trials with only 4 replicas that did successfully write trajectories and perform exchanges but the full 72 replica run never seems to get moving. Any thoughts? Thank you, Dan -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Center of mass restraints
Thanks Justin, You're generous with your time, thank you. The coordinate file where all the ligand atoms are set to the COM coordinates, will that be pasted in place of the actual ligand coordinates in the "complex.gro" file or how do I incorporate that into the run? Dan On Mon, Nov 11, 2019 at 7:18 PM Justin Lemkul wrote: > > > On 11/11/19 3:58 PM, Daniel Burns wrote: > > Thank you! > > > > If I use the coordinates of the center of mass for the spherical > restraint, > > will the ligand remain restrained to that coordinate if the protein > rotates > > or translates the binding site away from that original position? > > No, that's only possible with the pull code. If you're just trying to do > a simple pose refinement, you could apply a light restraint on the > backbone or C-alpha atoms to prevent this from happening. > > > Or am I > > going about this wrong? Can I set up that spherical restraint with a > > genrestr command without calculating the coordinates of the center of > mass > > from a visualization software? > > genrestr won't generate what you need. > > Obtain the COM coordinates of your desired residues with gmx traj -ox > -com and a suitable index group. That's the origin of the restraint. > Create a (physically unrealistic) coordinate file where all the ligand > atoms are set to those coordinates. > > > I haven't been able to find an example of this. > > Probably good fodder for my next tutorial...there are lots of practical > applications to using the flat-bottom restraints. > > -Justin > > > On Mon, Nov 11, 2019 at 8:25 AM Justin Lemkul wrote: > > > >> > >> On 11/10/19 2:54 PM, Daniel Burns wrote: > >>> Hello, > >>> > >>> I have identified a set of amino acid residues that surround a small > >>> molecule binding site. How would I go about restraining the small > >> molecule > >>> ligand to the center of mass of the surrounding residues? I want the > >>> molecule to be able to bounce around in the binding site to let if find > >> the > >>> most energetically favorable configuration. > >> You could either set up a spherical flat-bottom restraint with the > >> origin of that restraint coincident with the COM of the desired > >> residues, or you could use the pull code to set a restraint between the > >> COM of the protein residues and the COM of the ligand. > >> > >> -Justin > >> > >> -- > >> == > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> == > >> > >> -- > >> 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 gmx-users-requ...@gromacs.org. > >> > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Center of mass restraints
Thank you! If I use the coordinates of the center of mass for the spherical restraint, will the ligand remain restrained to that coordinate if the protein rotates or translates the binding site away from that original position? Or am I going about this wrong? Can I set up that spherical restraint with a genrestr command without calculating the coordinates of the center of mass from a visualization software? I haven't been able to find an example of this. On Mon, Nov 11, 2019 at 8:25 AM Justin Lemkul wrote: > > > On 11/10/19 2:54 PM, Daniel Burns wrote: > > Hello, > > > > I have identified a set of amino acid residues that surround a small > > molecule binding site. How would I go about restraining the small > molecule > > ligand to the center of mass of the surrounding residues? I want the > > molecule to be able to bounce around in the binding site to let if find > the > > most energetically favorable configuration. > > You could either set up a spherical flat-bottom restraint with the > origin of that restraint coincident with the COM of the desired > residues, or you could use the pull code to set a restraint between the > COM of the protein residues and the COM of the ligand. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
[gmx-users] Center of mass restraints
Hello, I have identified a set of amino acid residues that surround a small molecule binding site. How would I go about restraining the small molecule ligand to the center of mass of the surrounding residues? I want the molecule to be able to bounce around in the binding site to let if find the most energetically favorable configuration. Thank you! Dan -- 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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] Duplicated dihedral lines on .prm file
Thank you! Should my ligands have identical names in the .gro file? On Fri, Nov 8, 2019 at 6:23 PM Justin Lemkul wrote: > > > On 11/8/19 4:25 PM, Daniel Burns wrote: > > Hello, > > > > I am trying to simulate a dimer with identical ligands bound on each > > subunit. > > > > I generated the ligand files with cgenff. > > > > I have Liga and Ligb files that each have identical contents (the > > filenames, residue, and molecule name are different though). I am only > > getting errors on the Ligb.prm file in the [dihedral types] section. The > > problematic section repeats the i, j, k, and l atoms for 3 or more lines > > but each line has different phi and kphi values. The error is shown > below > > along with the section of the ligb.prm file that presents the issue. > > > > > > Thank you for your time! > > > > Dan > > > > ERROR 9 [file ligb.prm, line 42]: > > > >Encountered a second block of parameters for dihedral type 9 for the > same > > > >atoms, with either different parameters and/or the first block has > > > >multiple lines. This is not supported. > > > > > > The troublesome lines from ligb.prm: > > > > > > CG2R61 CG2R61CG321 NG2R51 9 0.00 0.497896 2 > >CG2R61 CG2R61CG321 NG2R51 9 180.00 0.552288 > 4 > >CG2R61 CG2R61CG321 NG2R51 9 180.00 0.054392 > 6 > >CG2R61CG321 NG2R51 CG2R51 9 0.00 1.610840 > 1 > >CG2R61CG321 NG2R51 CG2R51 9 0.00 1.757280 > 2 > >CG2R61CG321 NG2R51 CG2R51 9 0.00 0.334720 > 3 > >CG2R61CG321 NG2R51 CG2R51 9 0.00 0.230120 > 4 > >CG2R61CG321 NG2R51 NG2R50 9 180.00 1.610840 > 1 > >CG2R61CG321 NG2R51 NG2R50 9 0.00 1.757280 > 2 > >CG2R61CG321 NG2R51 NG2R50 9 180.00 0.334720 > 3 > >CG2R61CG321 NG2R51 NG2R50 9 0.00 0.230120 > 4 > > If the ligands are topologically identical, their bonded parameters can > only appear once in the topology. You can't simply #include both > topologies (despite giving them different [moleculetype] names) because > their bonded parameters will be repeated, therefore triggering this error. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
[gmx-users] Duplicated dihedral lines on .prm file
Hello, I am trying to simulate a dimer with identical ligands bound on each subunit. I generated the ligand files with cgenff. I have Liga and Ligb files that each have identical contents (the filenames, residue, and molecule name are different though). I am only getting errors on the Ligb.prm file in the [dihedral types] section. The problematic section repeats the i, j, k, and l atoms for 3 or more lines but each line has different phi and kphi values. The error is shown below along with the section of the ligb.prm file that presents the issue. Thank you for your time! Dan ERROR 9 [file ligb.prm, line 42]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. The troublesome lines from ligb.prm: CG2R61 CG2R61CG321 NG2R51 9 0.00 0.497896 2 CG2R61 CG2R61CG321 NG2R51 9 180.00 0.552288 4 CG2R61 CG2R61CG321 NG2R51 9 180.00 0.054392 6 CG2R61CG321 NG2R51 CG2R51 9 0.00 1.610840 1 CG2R61CG321 NG2R51 CG2R51 9 0.00 1.757280 2 CG2R61CG321 NG2R51 CG2R51 9 0.00 0.334720 3 CG2R61CG321 NG2R51 CG2R51 9 0.00 0.230120 4 CG2R61CG321 NG2R51 NG2R50 9 180.00 1.610840 1 CG2R61CG321 NG2R51 NG2R50 9 0.00 1.757280 2 CG2R61CG321 NG2R51 NG2R50 9 180.00 0.334720 3 CG2R61CG321 NG2R51 NG2R50 9 0.00 0.230120 4 -- 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 gmx-users-requ...@gromacs.org.
