Re: [gmx-users] Fatal Error when launching gromacs 2019.2 on GPU.
Hi, Thanks, setting this variable allowed me to start GROMACS without errors using the CPU. The problem is that this method prevents me from using other free GPUs on the host, but I would like to do this. I also found out that setting the CUDA_VISIBLE_DEVICE variable to available GPUs at the time of launch allows us to solve this problem. Artem On Sat, Oct 26, 2019 at 1:50 AM Szilárd Páll wrote: > Hi, > > This is an issue in one of pre-detection checks that trips due to > encountering exclusive / prohibited mode devices. > > You can work around this by entirely disabling the detection using the > GMX_DISABLE_GPU_DETECTION environment variable. > > Cheers, > -- > Szilárd > > > On Thu, Oct 17, 2019 at 5:01 PM Artem Shekhovtsov < > job.shekhovt...@gmail.com> > wrote: > > > Hello! > > Problem: The launch of mdrun that does not require video cards exit with > > fatal error if at least one video card is busy on the host at that time. > > gmx mdrun -deffnm test -ntmpi 1 -ntomp 1 -nb cpu -bonded cpu > > --- > > Program: gmx mdrun, version 2019.2 > > Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 100) > > > > Fatal error: > > cudaFuncGetAttributes failed: all CUDA-capable devices are busy or > > unavailable > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > --- > > > > I have this error in gromacs version 2019.2, 2019.3, 2020.beta. > > Version - 2018.6 is not affected. > > All version builds with the same flags. > > > > Archive with log files and gromacs build files > > > > > https://drive.google.com/file/d/1ahn7S69CU5yvAPlLWHryXmMzcGfdWVxP/view?usp=sharing > > > > > > I would appreciate any help. > > > > Thanks, > > Artem Shekhovtsov. > > -- > > 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] Fatal Error when launching gromacs 2019.2 on GPU.
Hello! Problem: The launch of mdrun that does not require video cards exit with fatal error if at least one video card is busy on the host at that time. gmx mdrun -deffnm test -ntmpi 1 -ntomp 1 -nb cpu -bonded cpu --- Program: gmx mdrun, version 2019.2 Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 100) Fatal error: cudaFuncGetAttributes failed: all CUDA-capable devices are busy or unavailable For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I have this error in gromacs version 2019.2, 2019.3, 2020.beta. Version - 2018.6 is not affected. All version builds with the same flags. Archive with log files and gromacs build files https://drive.google.com/file/d/1ahn7S69CU5yvAPlLWHryXmMzcGfdWVxP/view?usp=sharing I would appreciate any help. Thanks, Artem Shekhovtsov. -- 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] Inconsistent shifts over periodic boundaries error.
Hello! I performed simulations with the small molecules in water and faced with the fact that in about 5% of cases, the simulation falls at the last step with an error: --- Program: gmx mdrun, version 2018.4 Source file: src/gromacs/pbcutil/mshift.cpp (line 906) Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 47 atoms. The longest distance involved in such interactions is 1.298 nm which is close to half the box length. This molecule type consists of multiple parts, e.g. monomers, that are connected by interactions that are not chemical bonds, e.g. restraints. Such systems can not be treated. The only solution is increasing the box size. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The problem occurs when simulating in a rhombic dodecahedron cell with the standard distance between solute and the box 1nm. There is no such error in the cubic cell with distance 1nm. Trying to establish the reason for this behavior, I found that it is associated with the presence of virtual atoms in a small molecule. When I exchange a virtual atom for an atom linked by a chemical bond to the rest of the molecule, an error does not appear. I want to remove errors while preserving virtual atoms as well as the size and shape of the cell. Maybe someone already encountered this behavior and knows what my mistake is. I will be glad of any help. The link https://drive.google.com/file/d/0B5NzD-LVrUalbDdSblhfTkowUDN1aWxER3hlLWhaRFROcjhj/view?usp=sharing contains files for 1-step molecular dynamics that failed with my system of interest. Gromacs version - 2018.4. Thank you, Artem Shekhovtsov -- 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] FW: Free energy of solvation using the Bar method
Hello, Try to swap vdw_lambdas and coul_lambdas in *.mdp file like this: coul_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 vdw_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 Possible explanation: http://www.alchemistry.org/wiki/Constructing_a_Pathway_of_Intermediate_States#Avoid_turning_off_charges_and_Lennard-Jones_sites_at_the_same_time Best regards, Shekhovtsov Artem On Mon, Jun 3, 2019 at 5:23 PM Innocenti Malini, Riccardo < riccardo.innocentimal...@empa.ch> wrote: > > Dear all, > > I am currently trying to calculate the free energy of solvation for a > small hydrophobic molecule in water using the OPLSaa force field, however > for vdw lambda values above 0.2 my system continuously explodes. > > Before starting the free energy calculations I equilibrated the system > (100 ps in NVT and 4 ns in NPT ensemble). Then before starting the free > energy calculations before each lambda point I minimized the energy using > first the steepest descent method and then L-BFGS. The system is then > simulated in the NVT ensemble where it tends to blows when the vdw for > Lambda = 0.3. Below this value the system works fine in simulations of up > to 8 ns and the system appears to be equilibrated. > > I am not sure why this is happening. Would anybody have any advice? Here > is the free energy section of the mdp file: > > free_energy = yes > couple-moltype = Other > couple-lambda0 = vdw-q > couple-lambda1 = none > couple-intramol = no > init-lambda = -1 > init_lambda_state= 3 > delta_lambda = 0 > nstdhdl = 10 > fep-lambdas = > mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 > coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 0.15 > 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 > 0.95 1.00 > vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 > 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 1.00 > 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 > 1.00 1.00 > bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 > restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 > temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 0.00 > calc_lambda_neighbors= 1 > init-lambda-weights = > dhdl-print-energy= no > sc-alpha = 0.5 > sc-power = 1 > sc-r-power = 6 > sc-sigma = 0.3 > sc-coul = no > separate-dhdl-file = yes > dhdl-derivatives = yes > dh_hist_size = 0 > dh_hist_spacing = 0.1 > > Thank you in advance for your help. > > Kind regards, > Riccardo > > -- > 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] Bennet error in FEP-calculations for charged ligands.
Michael, Thank you so much for such a quick and detailed response. I tried to increase the number of intermediate lambda windows, but unfortunately, it was not possible to reduce the error to an acceptable level. coul-lambdas = 0.0 0.02 0.05 0.08 0.12 0.16 0.2 0.3 0.4 0.6 0.7 0.8 0.84 0.88 0.92 0.95 0.98 1.0 point 0 - 1, DG 47.68 +/- 0.13 point 1 - 2, DG 34.31 +/- 0.56 point 2 - 3, DG 19.42 +/- 0.97 point 3 - 4, DG 15.56 +/- 1.07 point 4 - 5, DG 8.45 +/- 0.03 point 5 - 6, DG 3.53 +/- 0.02 point 6 - 7, DG 4.99 +/- 0.02 point 7 - 8, DG 2.30 +/- 0.02 point 8 - 9, DG -0.02 +/- 0.03 point 9 - 10, DG -2.79 +/- 0.31 point 10 - 11, DG -5.74 +/- 0.72 point 11 - 12, DG -6.58 +/- 0.45 point 12 - 13, DG -8.02 +/- 0.03 point 13 - 14, DG -8.60 +/- 0.03 point 14 - 15, DG -15.92 +/- 0.04 point 15 - 16, DG -33.08 +/- 1.38 point 16 - 17, DG -47.34 +/- 1.22 total 0 - 17, DG 8.15 +/- 1.69 As for the three-level transformation, I agree that it should help, but it seems I don’t quite understand how to implement this behavior in GROMACS. I don't know by which options of the .mdp file it should be implemented and how to build topology files for such transformations. If you provided me with a small example of an mdp and itp file for such a transformation, I would be very grateful to you. Thank you, Shekhovtsov Artem On Wed, Jan 23, 2019 at 7:00 PM Michael Shirts wrote: > As free energies get larger, then the error gets less accurate. So if it is > reporting 18.51 +/- 2.95 for one of the intervals, that likely suggest > there is very little overlap in that area. > A total free energy difference of in -6.12 +/- 3.19 for the > transformation indicates that the result is not very certain; you're within > two standard deviations, and again, the Bennett error formula is inaccurate > for larger error. I would suggest adding 1-2 more intermediates between > those points. > > https://github.com/MobleyLab/alchemical-analysis provides some of the > tools > to check overlap. > > I would also suggest doing a multi stage transformation to increase overlap > - for atoms that are disappearing or appearing that are charged, turn off > charges off, change vdw, then turn charges back on. In some cases, > especially when the atoms involved have different sizes, sc-coul can lead > to some semi-pathological cases when vdw softcore and coul softcore result > in some very low/high potentials at intermediates. > > On Wed, Jan 23, 2019 at 8:21 AM Artem Shekhovtsov < > job.shekhovt...@gmail.com> > wrote: > > > Hi all! > > I encountered an error in my relative free energy calculations and do not > > know how to fix it. > > Molecules for which I want to carry out calculations contain a carboxyl > > group. > > To validate the protocol, I tried to run the fep-calculations of > symmetric > > molecules for which the change in free energy will be zero. > > During validation, I was faced with the fact that the convergence error > for > > charged ligands greatly exceeds that for neutral ones. > > For example, for the case of m-methyl benzoic acid [O-]C(= O)c1cc(C)ccc1: > > Mutation (-CH3 + H) for one meta position (-H + CH3) for another meta > > position relative to the carboxyl group. > > > > Ionized acid (solvent leg, 5 ns): > > point 0 - 1, DG 28.74 +/- 0.02 > > point 1 - 2, DG 53.79 +/- 0.41 > > point 2 - 3, DG 27.76 +/- 2.45 > > point 3 - 4, DG 18.51 +/- 2.95 > > point 4 - 5, DG 8.80 +/- 0.79 > > point 5 - 6, DG 4.04 +/- 0.07 > > point 6 - 7, DG -0.06 +/- 0.04 > > point 7 - 8, DG -2.62 +/- 0.33 > > point 8 - 9, DG -8.95 +/- 0.27 > > point 9 - 10, DG -23.89 +/- 1.61 > > point 10 - 11, DG -29.32 +/- 1.29 > > point 11 - 12, DG -54.15 +/- 0.08 > > point 12 - 13, DG -28.79 +/- 0.03 > > > > total 0 - 13, DG -6.12 +/- 3.19 > > > > Unionized acid (solvent leg, 5 ns): > > point 0 - 1, DG 0.08 +/- 0.01 > > point 1 - 2, DG -6.88 +/- 0.10 > > point 2 - 3, DG -14.69 +/- 0.05 > > point 3 - 4, DG -21.07 +/- 0.03 > > point 4 - 5, DG -13.21 +/- 0.02 > > point 5 - 6, DG -7.46 +/- 0.02 > > point 6 - 7, DG -0.09 +/- 0.03 > > point 7 - 8, DG 7.37 +/- 0.02 > > point 8 - 9, DG 13.24 +/- 0.03 > > point 9 - 10, DG 21.15 +/- 0.
[gmx-users] Bennet error in FEP-calculations for charged ligands.
Hi all! I encountered an error in my relative free energy calculations and do not know how to fix it. Molecules for which I want to carry out calculations contain a carboxyl group. To validate the protocol, I tried to run the fep-calculations of symmetric molecules for which the change in free energy will be zero. During validation, I was faced with the fact that the convergence error for charged ligands greatly exceeds that for neutral ones. For example, for the case of m-methyl benzoic acid [O-]C(= O)c1cc(C)ccc1: Mutation (-CH3 + H) for one meta position (-H + CH3) for another meta position relative to the carboxyl group. Ionized acid (solvent leg, 5 ns): point 0 - 1, DG 28.74 +/- 0.02 point 1 - 2, DG 53.79 +/- 0.41 point 2 - 3, DG 27.76 +/- 2.45 point 3 - 4, DG 18.51 +/- 2.95 point 4 - 5, DG 8.80 +/- 0.79 point 5 - 6, DG 4.04 +/- 0.07 point 6 - 7, DG -0.06 +/- 0.04 point 7 - 8, DG -2.62 +/- 0.33 point 8 - 9, DG -8.95 +/- 0.27 point 9 - 10, DG -23.89 +/- 1.61 point 10 - 11, DG -29.32 +/- 1.29 point 11 - 12, DG -54.15 +/- 0.08 point 12 - 13, DG -28.79 +/- 0.03 total 0 - 13, DG -6.12 +/- 3.19 Unionized acid (solvent leg, 5 ns): point 0 - 1, DG 0.08 +/- 0.01 point 1 - 2, DG -6.88 +/- 0.10 point 2 - 3, DG -14.69 +/- 0.05 point 3 - 4, DG -21.07 +/- 0.03 point 4 - 5, DG -13.21 +/- 0.02 point 5 - 6, DG -7.46 +/- 0.02 point 6 - 7, DG -0.09 +/- 0.03 point 7 - 8, DG 7.37 +/- 0.02 point 8 - 9, DG 13.24 +/- 0.03 point 9 - 10, DG 21.15 +/- 0.06 point 10 - 11, DG 14.72 +/- 0.03 point 11 - 12, DG 6.98 +/- 0.07 point 12 - 13, DG -0.05 +/- 0.01 total 0 - 13, DG 0.09 +/- 0.22 For a neutral molecule containing a charged carboxyl and amino groups ([O-]C(=O)c1cc(C)c([NH3+])cc1) the error is small: point 0 - 1, DG -4.65 +/- 0.01 point 1 - 2, DG -19.95 +/- 0.04 point 2 - 3, DG -28.67 +/- 0.13 point 3 - 4, DG -57.84 +/- 0.19 point 4 - 5, DG -44.18 +/- 0.08 point 5 - 6, DG -26.84 +/- 0.05 point 6 - 7, DG 0.10 +/- 0.20 point 7 - 8, DG 26.92 +/- 0.06 point 8 - 9, DG 44.28 +/- 0.13 point 9 - 10, DG 57.79 +/- 0.13 point 10 - 11, DG 28.68 +/- 0.09 point 11 - 12, DG 19.98 +/- 0.12 point 12 - 13, DG 4.66 +/- 0.03 total 0 - 13, DG 0.28 +/- 0.21 Adding Na and Cl ions to ([O-]C(=O)c1cc(C)c([NH3+])cc1) does not cause an increase in error. point 0 - 1, DG -4.61 +/- 0.01 point 1 - 2, DG -19.96 +/- 0.07 point 2 - 3, DG -28.68 +/- 0.04 point 3 - 4, DG -57.67 +/- 0.04 point 4 - 5, DG -44.24 +/- 0.01 point 5 - 6, DG -26.91 +/- 0.04 point 6 - 7, DG 0.03 +/- 0.03 point 7 - 8, DG 26.89 +/- 0.03 point 8 - 9, DG 44.20 +/- 0.08 point 9 - 10, DG 57.75 +/- 0.09 point 10 - 11, DG 28.65 +/- 0.06 point 11 - 12, DG 20.02 +/- 0.05 point 12 - 13, DG 4.67 +/- 0.01 total 0 - 13, DG 0.12 +/- 0.18 FEP-part of *.mdp: free-energy = yes sc-power = 1 sc-alpha = 0.5 sc-coul = yes fep-lambdas = 0.0 0.01 0.05 0.1 0.2 0.3 0.4 0.6 0.7 0.8 0.9 0.95 0.99 1.0 coul-lambdas = 0.0 0.01 0.05 0.1 0.2 0.3 0.4 0.6 0.7 0.8 0.9 0.95 0.99 1.0 vdw-lambdas = 0.0 0.01 0.05 0.1 0.2 0.3 0.4 0.6 0.7 0.8 0.9 0.95 0.99 1.0 What is the reason of such error and how I can fix it? mdp, itp, gro, xvg files by link - https://drive.google.com/open?id=1MiepOQb2QAZ9rclpY13owCnl8QWcTHnf Ready to provide any additional information. Thank you, Shekhovtsov Artem -- 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] Different coefficients for 1-4 pairs of nonbonded interactions.
Hello! I was faced with the need to use different coefficients for 1-4 nonbonded interactions. Some pairs in the molecule use a coefficient 0.5 for LJ and Coulomb interactions, others use a coefficient 0.833. I can use the [pairtypes] section to change the LJ coefficients, but this will not allow me to do the same for Coulomb interactions. How can I implement this behavior in gromacs and is it possible at all? Thank you, Artem Shekhovtsov. -- 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.
