[gmx-users] spliting of long trajectories to generate many small trajectories
Hi all Can a long md trajectory be split into into small trajectories of equal length to apply markov state modelling on it using gromacs? Thank you all in advance. -- 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] Fwd: restraints failure problem
Dear Gromacs users I am posting this problem third time in hope to get some suggestions regarding my problem. I am doing a test calculation in MD simulation between ligand and a protein residue for bond angle and dihedral restraints. I have set them in my topology file as below:- ; distance restraints [ bonds ] ;ij type r0A r1A r2AfcAr0B r1B r2BfcB 712910 0.403 0.403 10.0 0.00.403 0.403 10.0 4184.000 [ angle_restraints ] ; aiajakal typethA fcAmultA thB fcB multB 29716971 1 104.92 0.01 104.92 41.840 1 71293129 1 147.02 0.01 147.02 41.840 1 [ dihedral_restraints ] ; aiajakal typephiA dphiA fcAphiB dphiB fcB 69712931 1146.72 0.00.0 146.72 0.0 41.840 7271 2931 1 17.55 0.00.017.55 0.0 41.840 7271 2925 1 173.10 0.00.0 173.10 0.0 41.840 However, after energy minimization, I observed that my restraints are not working and I find the following change:- bonds changed from 0.403 *0.401* angles:- 104.92 changed to *107.98* 147.02 changed to *152.76* dihedrals:- 146.72 changed to *141.72* 17.55 changed to 2*2.13* 173.10 changed to *174.23* The fluctuation in restraints goes on increasing till the production run which shows that my restraints are not working. How should I work with these so that they may not change much? Do I need to increase force for restraints if yes then how much increase? any idea? I have tried these simulations with position restraints. Is the method of putting restraints correct or should I try some other? I have to apply these in the free energy calculation which already crashed because of restraint failure. I would really be thankful for your kind suggestions, please. 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.
[gmx-users] How to calculate the dihedral angle as a function of time?
Dear Gromacs users I want to calculate the dihedral angle over the simulation time. I tried following commands:- gmx mk_angndx -s topol.tpr -type dihedral which generates an index file for dihedral angles then running:- gmx angle -f md_prod.trr -n angle.ndx -type dihedral gives following group options, How can I identify these groups show which part of the system. I want to calculate the dihedral angle as a function of time in the simulation. Group 0 ( Phi=0.0_3_0.65) has 228 elements Group 1 ( Phi=0.0_1_0.84) has 8 elements Group 2 ( Phi=0.0_2_0.84) has 8 elements Group 3 ( Phi=0.0_3_1.67) has16 elements Group 4 ( Phi=0.0_3_0.67) has52 elements Group 5 ( Phi=0.0_1_1.05) has96 elements Group 6 ( Phi=0.0_3_0.70) has 4 elements Group 7 (Phi=180.0_2_10.46) has32 elements Group 8 ( Phi=0.0_1_8.37) has16 elements Group 9 ( Phi=0.0_2_8.37) has 8 elements Group10 ( Phi=0.0_2_1.13) has 8 elements Group11 ( Phi=0.0_3_1.76) has 8 elements Group12 (Phi=180.0_1_1.88) has 4 elements Group13 (Phi=180.0_2_6.61) has 4 elements Group14 (Phi=180.0_3_2.30) has 4 elements Group15 ( Phi=0.0_1_3.35) has 4 elements Group16 (Phi=180.0_3_0.33) has 4 elements Group17 (Phi=180.0_2_15.17) has96 elements Group18 ( Phi=0.0_3_0.75) has 8 elements Group19 (Phi=180.0_2_1.05) has20 elements Group20 (Phi=180.0_1_0.84) has20 elements Group21 ( Phi=0.0_3_0.63) has32 elements Group22 ( Phi=0.0_2_3.35) has12 elements Group23 ( Phi=0.0_3_0.67) has28 elements Group24 ( Phi=0.0_3_0.70) has20 elements Group25 ( Phi=0.0_3_0.60) has24 elements Group26 ( Phi=0.0_2_4.92) has24 elements Group27 ( Phi=0.0_3_0.65) has96 elements Group28 ( Phi=0.0_3_1.60) has24 elements Group29 ( Phi=0.0_3_1.60) has12 elements Group30 (Phi=180.0_2_0.42) has12 elements Group31 ( Phi=0.0_3_0.75) has12 elements I tried gmx chi also by the following command:- gmx chi -s md.gro -f md.xtc -all 1 -o dihedral.xvg The out put file indicate following information xaxis label "Residue" yaxis label "S2" What is S2 on y-axis. How should I interpret it? Could anyone please help me with this? I would really appreciate your kind suggestions. 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.
[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] GPU considerations for GROMACS
Hi, Whether investing in one of the fastest or two medium-high end GPU depends on your workload: system size, type of run, single or multiple simulations, etc. If you have multiple simulations you can run independently or coupled only weakly in ensemble runs (e.g. using -multidir), multiple mid-tier GPUs will be a better investment. On the other hand, if single simulation performance is what you want to maximize and you have a relatively small simulation system (e.g. 50k atoms), you will be better off with a single fast GPU. Regarding your CPU choice, I suggest you consider alternatives: e.g. a Ryzen 3800X will cost a lot less and will be faster. Xeon generally does not have much benefit for the use-case in question. Cheers, -- Szilárd On Tue, Feb 18, 2020 at 3:21 PM hairul.ik...@gmail.com < hairul.ik...@gmail.com> wrote: > Hello, > > Previously, I have helped building a workstation for my fellow > researcher who heavily uses GROMACS for his MD simulations, with the > following base specs: > > -CPU: 8 cores (Xeon E2278G) > -RAM: 32GB > -GPU: 1x RTX2080Ti > > > With this setup, he managed to shrink down each simulation runtime to, > say approximately 12 hours, compared to previous system (purely CPU > only, no GPU support), which took days to complete. > > > 1) Based on the current progress, we plan to build another system > (which will also run GROMACS most of the time) using the existing > workstation as reference. But currently we are unsure which setup > (Option 1 vs Option 2) will GENERALLY give shortest/fastest runtime, > when running the same set of GROMACS simulation : > > > Option 1: > Retain same CPU, RAM and GPU specs (1x RTX2080Ti) > > > Option 2: > Retain same CPU and RAM specs, but GPU wise, use 2x RTX 2070S instead > of 1x RTX2080Ti > > > 2) Besides building another system, we are considering to upgrade the > existing system, too. For example, assuming the system has the > expansion capability (enough PCI-e 16x slots, power supply), will > adding another card (making it 2x RTX2080Ti instead of 1x RTX2080Ti) > into existing setup will significantly cut down current runtime? If > yes, by how much time reduction can we expect generally with this > upgrade? > > > Appreciate if someone can share their thoughts and experience. > Thank you! > > > -Hairul > -- > 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.
