A couple of things: 1. Are your cutoffs appropriate for OPLS_AA? Even if you fix any code problems and using the wrong cutoffs, your results will not be meaningful... 2. How are you generating your box/filling it with molecules? There are indications that your original box is too small, or that there are clashing atoms in the original configuration, since with a much bigger box you don't seem to have problems except for particles moving too rapidly for domain decomposition to handle (perhaps there is a cutoff/coupling problem). 2b: what is atom 13090 and what is in its vicinity? ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of emmanuelle [e.a.y.m...@student.tudelft.nl] Sent: Thursday, December 20, 2012 2:31 PM To: gmx-users@gromacs.org Subject: [gmx-users] Energy Minimization/ NpT settling problem
Hi, I am trying to simulate a system consisting of 1790 molecules of monoethanolamine (MEA), 203 molecules of CO2 and 18210 molecules of water. After having generated my box and set the density to 1000g/l using editconf, I am facing a problem with the energy minimization step. It does not converge to the tolerence I give (Fmax<500kJ/mol). I get this message: Steepest Descents converged to machine precision in 199 steps, but did not reach the requested Fmax < 500. Potential Energy = -9.27407663461033e+05 Maximum force = 2.07667591793109e+06 on atom 13090 Norm of force = 1.06912622245517e+04 Since no problem occurs when I simulate CO2 with water only, I think the problem comes from MEA for which I apply an OPLS_AA force field. I tried lots of different initial configurations for MEA, using structures developed with the Avogadro program and structures from data bank found on the net. All of them result in the same convergence problem. I don't think there is an issue in my mdp file as I use it for other simulations which work well. It is as follow: title = Minimization ; Title of run define =-DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 500.0 ; Stop minimization when the maximum force < 500.0 kJ/mol emstep = 0.001 ; Energy step size nsteps = 100000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) I also tried another approach: I inserted the molecules in a much more bigger box and performed the energy minimization of this system with a very low density. This could converge. Afterwards, I run an npT simulation with a high pressure (10 bar) such that the box shrinks and that the system reachs the good density. At that step, the following error came out: Making 1D domain decomposition 12 x 1 x 1 starting mdrun 'CO2 in MEA at 303K' 5000 steps, 5.0 ps. ^Mstep 0imb F 4% ^Mstep 100, remaining runtime: 132 s step 134: Water molecule starting at atom 24060 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates ------------------------------------------------------- Program mdrun_d, VERSION 4.5.5 Source code file: pme.c, line: 538 Fatal error: 1 particles communicated to PME node 7 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Can someone tell me where I am making any mistake and why is my system not converging? Thanks in advance, Emmanuelle MSc student -TU Delft -- View this message in context: http://gromacs.5086.n6.nabble.com/Energy-Minimization-NpT-settling-problem-tp5003976.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
