[gmx-users] DSSP graph re-scale
Dear experts, I have an issue to re-scale the x-axis on DSSP graph eps format for my 100 ns simulation time. The x-axis of the graph became too compact until it can't be read clearly. How should I solve this? Is there anyway to re-scale the graph for eps format. Your help is much appreciated. Thank you. Regards, Syah -- 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] Fat-bottom restrain
Hi Mark, Thank you for your response. Here are the part of options that gmx energy gives me out: 9 Coulomb-(SR)10 Coul.-recip. 11 Flat-bottom-posres 12 Potential 13 Kinetic-En. 14 Total-Energy15 Conserved-En Energy Average Err.Est. RMSD Tot-Drift --- Coulomb (SR) -8.4629e+061505041.75 -840.379 (kJ/mol) Coul. recip.12689.7 12109.811 -83.8453 (kJ/mol) Flat-bottom posres0 0 0 0 (kJ/mol) Potential-7.29781e+065403208.53 -3702.71 (kJ/mol) Kinetic En. 1.20527e+068.21912.61-12.144 (kJ/mol) Total Energy -6.09255e+06540 3942.5 -3714.84 (kJ/mol) Conserved En.-2.97263e+06 89 1.81911e+06 6.30101e+06 (kJ/mol) As can be seen above the Flat-bottom posres energy is just zero during the simulation; and even stiffening the force constant from 4184 KJ/(mol. nm^2) to 4184000 KJ/(mol. nm^2) doesn't change anythings and the Flat-bottom posres energy would remain absolutely zero! I rechecked everything and I don't see any problem with the way I have set the flat-bottom restrain. Any comment would be highly appreciated. Thank you, Alex On Sat, Sep 7, 2019 at 10:47 AM Mark Abraham wrote: > Hi, > > The total potential energy violating the restraints is reported, so you > should see that there is an appropriate contribution there, and probably > plan to stiffen the force constant. > > Mark > > On Fri., 6 Sep. 2019, 17:23 Alex, wrote: > > > Dear all, > > Using the flat-bottom (K=4184 KJ/(mol. nm^2)) restrain I tried to have a > > smaller cubic box as semi-preamble walls inside a bigger cubic box so > that > > all molecules except water would stay inside the smaller box during the > > simulation, however, the wall doesn't work and the molecules are also out > > of the smaller box in several replica's simulations each with 100 ns. > > The only reason I can imagine is that the K=4184 KJ/(mol. nm^2 is > probably > > too low to keep the molecules inside the smaller box! I wonder if you > know > > any other potential reason? how can I find out the reason? > > > > Regards, > > Alex > > P.S. I am sure that I am using the flat-bottom restrain correctly as the > > same approach worked for some other systems of mine previously. > > -- > > 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] Solvent is added inconsistently
Dear All, I am facing an issue I do not fully understand. Namely, let's take two crystallographic structures of the same protein and in one of them let's delete three crystallographic water molecules that are not buried inside the protein (let's forget about a reason for it for a moment). Now, when I use exactly the same procedure to generate the box and the solvent I get a slightly different number of solvent (water) molecules. This makes sense obviously, because after deleting the crystallographic water molecules, there is slightly more space to be filled. However I noticed that presence of some water molecules added by solvate and buried inside the protein cavities depends on whether these three initial water molecules were deleted or not. Why is that? I know that after deleting the water molecules the centering of my protein (with its remaining crystallographics water molecules) is somehow different but why does it affect the position and/or presence of some newly added water molecules? Best wishes, Dawid Grabarek PS I use gromacs 2016.3 PPS I use following commands: gmx pdb2gmx -f $name.pdb -o "$name".gro -p "$name".top -water tip3p -his -glu gmx editconf -f "$name".gro -o "$name"-box.gro -bt triclinic -d 1.2 -princ gmx solvate -cp "$name"-box.gro -cs spc216.gro -p "$name".top -o "$name"-solv.gro -- 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] optimizing GAFF2 torsional parameters
dear all, I am trying to improve the GAFF2 dihedral parameters for a torsion on a small molecule. My small molecule has 5 torsions, only one is problematic, I have been able to improve the dihedral parameters for the other 4 torsions by adjusting the force constants of the GAFF2 dihedral terms. In the figure shown here (PDF file): https://drive.google.com/file/d/1IkqoZ2CPEexZlAYt_DuQMqHzjGKWE6zK/view?usp=sharing red is QM, green is GAFF2, blue is one of my attempts to improve the results. The somewhat improved energy maximum at 0 degrees comes with an artificial minimum at around -30 degrees. This minimum seems to also be present at the default GAFF2 torsional profile but it is more shallow. I can increase the weights of the points around the artificial minimum to make them more consistent with QM data, but of course that comes at the expense of less agreement with QM data at around -180- -120 degrees. I have also tried optimizing the phase angles, without restricting them to 0 or 180, but that introduces an additional artificial energy minimum at around -150 degrees. I have also tried all possible multiplicities, 1,2,3 without any luck. I am using Mathematica to do the optimization. What strategies have people used in the past to improve agreement of dihedral parameters with QM data? Are there reasons to prefer no artificial energy minima versus better agreement on energy barriers? Best wishes, Christos Deligkaris, PhD Assistant Professor of Physics, University of Southern Indiana SC2220, 8600 University Blvd, Evansville IN, 47712 Office Phone: (812) 228-5056 www.deligkaris.org @DeligkarisGroup -- 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] Load imbalancing
Hi, On Mon, 9 Sep 2019 at 12:01, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Dear all, > I am running REMD simulation with 65 replicas. When the > simulation is running , I checked the .log file for every replica. In some > replicas I am getting more than 10% load imbalancing. How to solve that. That's common to all kinds of simulations, a geometric decomposition of the work of a simulation is going to have imbalance. How that arises and what if anything might be done is not related to REMD (Although e.g. NPT REMD can make it worse.) If > I use -ntmpi and -ntomp option ..mdrun is throwing a fatal error > > Fatal error: > Setting the number of thread-MPI ranks is only supported with thread-MPI > and > GROMACS was compiled without thread-MPI > > In the document ( > http://www.gromacs.org/Documentation/Acceleration_and_parallelization)...it > is mentioned that -ntmpi can not be used in multi-simulation runs. > So how i can avoid load imbalancing in remd simulations... > Changing the number of ranks does affect imbalance, but the relevant thing is how long you can afford to take rnning the simulation. Running one rank per simulation has no load imbalance, but lowest throughput. One can use -ntmpi to change the number of ranks, but as the error message says, that's only for a thread-MPI build, and you need a real MPI build to run REMD. Mark -- 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] Cannot run short-ranged nonbonded interactions on a GPU
Hi, What does the log file detection output contain? You might have linked against a CUDA release not compatible with your drivers (e.g. too recent). Cheers, -- Szilárd On Sun, Sep 8, 2019 at 5:17 PM Mahmood Naderan wrote: > > Hi > With the following config command > cmake .. -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=`pwd`/../single > -DGMX_BUILD_OWN_FFTW=ON > I get the following error for "gmx mdrun -nb gpu -v -deffnm inp_nvp" > Fatal error: > Cannot run short-ranged nonbonded interactions on a GPU because there is none > detected. > > > > deviceQuery command shows that GPU is detected. > $ ./deviceQuery > ./deviceQuery Starting... > > CUDA Device Query (Runtime API) version (CUDART static linking) > > Detected 1 CUDA Capable device(s) > > Device 0: "GeForce GTX 1080 Ti" > ... > > > With the same input, I haven't seen that error before. Did I miss something? > > Regards, > Mahmood > -- > 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] Load imbalancing
Dear all, I am running REMD simulation with 65 replicas. When the simulation is running , I checked the .log file for every replica. In some replicas I am getting more than 10% load imbalancing. How to solve that. If I use -ntmpi and -ntomp option ..mdrun is throwing a fatal error Fatal error: Setting the number of thread-MPI ranks is only supported with thread-MPI and GROMACS was compiled without thread-MPI In the document ( http://www.gromacs.org/Documentation/Acceleration_and_parallelization)...it is mentioned that -ntmpi can not be used in multi-simulation runs. So how i can avoid load imbalancing in remd simulations... -- 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.
