Hi Justin I obtained the following error with the following command and the mdp mentioned below
gmx mdrun -s 1_OGNG_GLYCAM_SPE_GMX.tpr -rerun 1_OGNG_Amber.pdb Thank you Stéphane ------------------------------------------------------------------ Program: gmx mdrun, version 2018.1 Source file: src/programs/mdrun/runner.cpp (line 736) Fatal error: The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors >> You also shouldn't use a minimizer when doing a zero-point energy. Use the >> md integrator. OK I try your suggestion ---------------------------------------------------------------------- And the mdp Message: 1 Date: Thu, 23 Apr 2020 06:18:33 -0400 From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion Message-ID: <28a2dc8e-20e9-abee-4b10-0f3cceb4f...@vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 4/23/20 5:42 AM, ABEL Stephane wrote: > Deal all, > > I am using acpype to convert a set of glycolipids modeled with the GLYCAM06 > force fiedl into the GROMACS format. acpype works well for this task. But I > would like to check if the conversion is correctly done by performing single > point energy (SPE) calculations with Amber and GROMACS codes and thus > computes the energy differences for the bonded and non bonded terms > > For the former test I using the prmtop and inpcrd files generated with tleap > and sander with the minimal commands below > > | mdin Single point > &cntrl > imin=0, > maxcyc=0, > ntmin=2, > ntb=0, > igb=0, > cut=999 > / > > But For GROMACS vers > 5.0 and 2018.x , I did not find the equivalent mdp > parameters that can be used for doing the same task. I I used the minimal > file below The bonded energy terms are very similar between the two codes but > not the non bonded terms > > integrator = steep ; Algorithm (steep = steepest descent > minimization) > emtol = 1000.0 ; Stop minimization when the maximum force < > 1000.0 kJ/mol/nm > emstep = 0.01 ; Minimization step size > nsteps = 0 ; Maximum number of (minimization) steps to perform > (should be 50000) > > ; 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 > cutoff-scheme = Group ; Buffered neighbor searching > ns_type = grid ; Method to determine neighbor list (simple, grid) > coulombtype = Cut-off ; Treatment of long range electrostatic > interactions > rcoulomb = 0 ; Short-range electrostatic cut-off > rvdw = 0 ; Short-range Van der Waals cut-off > rlist = 0 > pbc = no ; P > continuation = yes > > I also also notice that a tpr generated with this mdp can not be used with > -rerun argument so how I can compute a SPE equivalent to Sander Why is it incompatible with mdrun -rerun? Do you get an error? You also shouldn't use a minimizer when doing a zero-point energy. Use the md integrator. -Justin -- 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.
