Thanks Justin for looking at the files. I am using the gro and top file to generate a tpr with the following mdp file in order to see if everything is all right:
title = geometry-optimization cpp = /usr/bin/cpp include = integrator = steep comm_mode = Linear dt = 0.001 nsteps = 1000000 ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 1000 nstvout = 1000 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 xtc-precision = 100000 xtc_grps = System energygrps = System pbc = xyz nstlist = 10 epsilon_r = 1. ns_type = grid ; or grid I don't know coulombtype = pme vdwtype = Cut-off fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = yes rlist = 0.8 rcoulomb = 0.8 rvdw = 0.8 emtol = 1.0 Yes, I am dealing with single molecule of ethanol. I can attach the tpr file and the resulting trr and gro file but it seems that the file size is big. When I visualize the trajectory. in the second step, the molecule is already without any bond ... it is separated atoms. I don't think this is visualization problem since I already tried all trjconv -pbc option. I am very confused. Thank for helping G. From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Monday, September 2, 2013 1:34 PM Subject: Re: [gmx-users] adding ETHANOL to CGennFF in gromacs has problem Please make sure to keep the discussion on the mailing list. On 9/2/13 1:27 PM, Golshan Hejazi wrote: > This is the gro file that I am using: > ETHANOL > 9 > 1ETHA C1 1 3.133 3.266 0.008 > 1ETHA O1 2 3.244 3.350 -0.021 > 1ETHA HO1 3 3.324 3.296 -0.015 > 1ETHA H11 4 3.143 3.225 0.111 > 1ETHA H12 5 3.129 3.182 -0.065 > 1ETHA C2 6 3.007 3.351 -0.002 > 1ETHA H21 7 3.011 3.435 0.071 > 1ETHA H22 8 2.998 3.394 -0.104 > 1ETHA H23 9 2.917 3.290 0.019 > 3.41840 3.44350 3.38360 > > This is what I added in the rtp: > > [ ETHA ] > [ atoms ] > C1 CG321 0.05 0 > O1 OG311 -0.65 1 > HO1 HGP1 0.42 2 > H11 HGA2 0.09 3 > H12 HGA2 0.09 4 > C2 CG331 -0.27 5 > H21 HGA3 0.09 6 > H22 HGA3 0.09 7 > H23 HGA3 0.09 8 > [ bonds ] > C1 C2 > C1 O1 > C1 H11 > C1 H12 > O1 HO1 > C2 H21 > C2 H22 > C2 H23 > > And this is the resulting topology: > > ; Include forcefield parameters > #include "./charmm36.ff/forcefield.itp" > > [ moleculetype ] > ; Name nrexcl > drug 3 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass typeB > chargeB massB > ; residue 1 ETHA rtp ETHA q 0.0 > 1 CG321 1 ETHA C1 1 0.05 12.011 ; qtot >0.05 > 2 OG311 1 ETHA O1 2 -0.65 15.9994 ; qtot >-0.6 > 3 HGP1 1 ETHA HO1 3 0.42 1.008 ; qtot >-0.18 > 4 HGA2 1 ETHA H11 4 0.09 1.008 ; qtot >-0.09 > 5 HGA2 1 ETHA H12 5 0.09 1.008 ; qtot >0 > 6 CG331 1 ETHA C2 6 -0.27 12.011 ; qtot >-0.27 > 7 HGA3 1 ETHA H21 7 0.09 1.008 ; qtot >-0.18 > 8 HGA3 1 ETHA H22 8 0.09 1.008 ; qtot >-0.09 > 9 HGA3 1 ETHA H23 9 0.09 1.008 ; qtot >0 > [ bonds ] > ; ai aj funct c0 c1 c2 c3 > 1 2 1 > 1 4 1 > 1 5 1 > 1 6 1 > 2 3 1 > 6 7 1 > 6 8 1 > 6 9 1 > > [ pairs ] > ; ai aj funct c0 c1 c2 c3 > 2 7 1 > 2 8 1 > 2 9 1 > 3 4 1 > 3 5 1 > 3 6 1 > 4 7 1 > 4 8 1 > 4 9 1 > 5 7 1 > 5 8 1 > 5 9 1 > [ angles ] > ; ai aj ak funct c0 c1 c2 > c3 > 2 1 4 5 > 2 1 5 5 > 2 1 6 5 > 4 1 5 5 > 4 1 6 5 > 5 1 6 5 > 1 2 3 5 > 1 6 7 5 > 1 6 8 5 > 1 6 9 5 > 7 6 8 5 > 7 6 9 5 > 8 6 9 5 > > [ dihedrals ] > ; ai aj ak al funct c0 c1 c2 > c3 c4 c5 > 4 1 2 3 9 > 5 1 2 3 9 > 6 1 2 3 9 > 2 1 6 7 9 > 2 1 6 8 9 > 2 1 6 9 9 > 4 1 6 7 9 > 4 1 6 8 9 > 4 1 6 9 9 > 5 1 6 7 9 > 5 1 6 8 9 > 5 1 6 9 9 > > ; Include Position restraint file > #ifdef POSRES > #include "posre.itp" > #endif > > [ system ] > ; Name > ETHANOL > > [ molecules ] > ; Compound #mols > drug 1 > All of this looks perfectly normal. What are you trying to do when it flies apart? Are you dealing with a single molecule only? -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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
