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 Thanks in advance for your help and suggestions Stéphane -- 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.
