On Sat, Sep 9, 2017 at 2:09 AM, Abhishek Acharya <abhi117acha...@gmail.com> wrote:
> Dear GROMACS users, > > I am trying to estimate the free energy of solvation for a ion. But, I am > facing a problem while running simulations for the deltaG_LJ calculation. > The simulation at vdw_lambda=1.0 crashes during the steepest-descent > minimization step, with the following error. > > ------------------------------------------------------- > Program gmx mdrun, VERSION 5.1.2 > Source code file: > /home/bp-lab/Downloads/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: > 555 > > Fatal error: > > step 10: Water molecule starting at atom 120 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > The free energy parameters I used for this run are as follows: > ************************************************************ > ************************************************************* > free_energy = yes > couple-moltype = Protein > couple-lambda0 = vdw > couple-lambda1 = none > couple-intramol = no > init-lambda = -1 > init_lambda_state = 20 > 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 > 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 > 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 > 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 > 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 > 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 > 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 > ************************************************************ > ************************************************************* > > Out of curiosity, I also ran simulations for a reverse transformation with > the following parameters (and I hope they are correct): > > ************************************************************ > ************************************************************* > free_energy = yes > couple-moltype = Protein > couple-lambda0 = none > couple-lambda1 = vdw > couple-intramol = no > init-lambda = -1 > init_lambda_state = 0 > 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 > 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 > 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 > 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 > 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 > 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 > 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 > ************************************************************ > ************************************************************* > Intriguingly, I this case I got the exact error as above, but this time at > lambda=0. > That make sense, since in both cases the vdw interactions are off in both situations (couple-lambda0 or couple-lambda1 = none). > ------------------------------------------------------- > Program gmx mdrun, VERSION 5.1.2 > Source code file: > /home/bp-lab/Downloads/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: > 555 > > Fatal error: > > step 10: Water molecule starting at atom 120 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > LINCS has been used to constrain all-bonds with lincs_order = 12. > > Analysis of step10b.pdb and step10c.pdb did not reveal any obvious clashes > between water molecules. > > I have also run simulations for charge annihilation step and I did not face > such a problem. > Has the charge been turned off for this series of simulations? You should generally turn electrostatics off through a series of free energy simulations and then turn off VDW while the charge is off. > > Looking for the some advice on how to proceed from here. > I do something like this: vdw-lambdas = 0.00 0.00 0.00 0.00 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul-lambdas = 0.00 0.25 0.50 0.75 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 couple-lambda0 = vdw-q couple-lambda1 = none See: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html http://wbarnett.us/tutorials/4_methane_fe/ -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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