Hello gmx-users, I am having a problem with energy minimization of a DPPC bilayer and solvent. I have searched the archives for a good long while to help solve my problem, but so far I have had no luck. The system I am building consists of the bilayer and solvent molecules (water), in preparation for the insertion of a membrane protein. I have successfully done energy minimization on the bilayer with crystal waters. I added additional water molecules to appropriately solvate my protein, once it is inserted. When I try to run energy minimization on my solvent (to remove any bad contacts between crystal waters and additional solvent molecules, etc), I am consistently met with this error from mdrun:
Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1000. Potential Energy = 5.9483964e+18 Maximum force = inf on atom 6710 Norm of force = nan My .mdp file is this: ; The following lines tell the program the standard locations where to find certain files cpp = /usr/bin/cpp ; Preprocessor include = -I./ ; Directories to include in the topology format ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) dt = 0.002 ; Time step in ps emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform xtc_grps = system ; Which coordinate group(s) to write to disk energygrps = system ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 0 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, grid) rlist = 0.9 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb = 0.9 ; long range electrostatic cut-off rvdw = 0.9 ; long range Van der Waals cut-off pbc = no ; Periodic Boundary Conditions (yes/no) ; Parameters for temperature and pressure tau_t = 0.1 tc-grps = system ref_t = 323 ref_p = 1.0 I apologize if this is a trivial question (I am still a newbie to Gromacs), and I know that a number of similar issues have been discussed, but I would be forever grateful for some assistance in getting this issue resolved. Thanks in advance, Justin Justin A. Lemkul Undergraduate Researcher Department of Biochemistry Virginia Tech _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
