Dear GMX users, I am facing problem while doing energy minimization of the inflated system of a protein with membrane. I inflated the system and updated the removed lipids in the topology file. Now I am stuck during the energy minimization state. Below is the .mdp file for minimization.
--------------------------------------------------------------------- ; minim_1.mdp - used as input into grompp to generate em_1.tpr integrator = cg ; Algorithm (cg = conjugate gradient minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; Short-range electrostatic cut-off rvdw = 1.2 ; Short-range Van der Waals cut-off gen_vel = yes define = DSTRONG_POSRES when I run this using the command *grompp –f minim_1.mdp –c system_inflated.gro topol.top –o em_1.tpr * it generates the em_1.tpr file but does not generate any md_out.mdp file and it gives the following 2 notes Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6# checking input for internal consistency... processing topology... *NOTE 1 [file topol.top, line 24414]:* ** System has non-zero total charge: 1.400002e+01 processing coordinates... double-checking input for internal consistency... Reading position restraint coords from system_inflated.gro renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: Opening library file /usr/local/Gromacs/share/top/aminoacids.dat There are: 121 OTHER residues There are: 408 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... Making dummy/rest group for T-Coupling containing 9931 elements Making dummy/rest group for Acceleration containing 9931 elements Making dummy/rest group for Freeze containing 9931 elements Making dummy/rest group for Energy Mon. containing 9931 elements Making dummy/rest group for VCM containing 9931 elements Number of degrees of freedom in T-Coupling group rest is 29790.00 Making dummy/rest group for User1 containing 9931 elements Making dummy/rest group for User2 containing 9931 elements Making dummy/rest group for XTC containing 9931 elements Making dummy/rest group for Or. Res. Fit containing 9931 elements Making dummy/rest group for QMMM containing 9931 elements Checking consistency between energy and charge groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 216x216x55, spacing 0.119 0.119 0.120 Estimate for the relative computational load of the PME mesh part: 0.96 *NOTE 2 [file aminoacids.dat, line 1]:* ** The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This run will generate roughly 116 Mb of data writing run input file... There were 2 notes gcq#22: "I Had So Many Problem, and Then I Got Me a Walkman" (F. Black) ------------------------------------------------------------------------------------------I understand the note 1 as I haven’t added the ions yet, so the system has charge. But I am confused about note 2, what changes can I make to .mdp file for the minimization to run smoothly. Thanks, Parul
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
