Re: [gmx-users] Energy cal from MD simulations
On 1/12/19 1:10 AM, Lod King wrote: Hi, I have obtained a 100 ns simulation using Amber. I would like to calculate the potential energy (VDW, COUL,ect) from the trajectory, below is my command. $gmx grompp -f test.mdp -p ../gromacs.top -n ../index.ndx -c ../300.pdb -o rerun.tpr -maxwarn 1 It is always dangerous (and usually wrong) to ever use -maxwarn. $gmx mdrun -rerun ../protein.trr -s rerun.tpr -g rerun.log -e rerun.edr $gmx energy -f rerun.edr -o test.xvg My question is: in this test.mdp file, should I specify any parameters that should be the same as I used when running MD using Amber. If you're looking to obtain an equivalent output, yes. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
[gmx-users] Energy cal from MD simulations
Hi, I have obtained a 100 ns simulation using Amber. I would like to calculate the potential energy (VDW, COUL,ect) from the trajectory, below is my command. $gmx grompp -f test.mdp -p ../gromacs.top -n ../index.ndx -c ../300.pdb -o rerun.tpr -maxwarn 1 $gmx mdrun -rerun ../protein.trr -s rerun.tpr -g rerun.log -e rerun.edr $gmx energy -f rerun.edr -o test.xvg My question is: in this test.mdp file, should I specify any parameters that should be the same as I used when running MD using Amber. Run parameters integrator = md nsteps = 50; dt = 0.002 ; 2 fs ; Output control nstxout = 1 ; nstvout = 1 ; nstfout = 0 ; nstxtcout = 1000 ; ;nstxout-compressed = 1000 ; nstenergy = 1000 ; nstlog = 1 ; ; Constraints constraint_algorithm = lincs; constraints = hbonds; d lincs_iter = 1 ; lincs_order = 4 ; continuation= yes ; ; Neighborsearching cutoff-scheme = Verlet; verlet-buffer-tolerance = 0.005 ; ns_type = grid ; nstlist = 20; rlist = 1.0 ; rcoulomb= 1.0 ; rvdw= 1.0 ; ; Electrostatics coulombtype = PME ; pme_order = 4 ; fourierspacing = 0.16 ; ; Temperature coupling is on tcoupl = V-rescale ; tc-grps = System; tau_t = 0.1 ; ref_t = 300 ; pcoupl = Parrinello-Rahman ; pcoupltype = isotropic ; tau_p = 2.0 ; ref_p = 1.0 ; compressibility = 4.5e-5; pbc = xyz ; DispCorr= EnerPres ; gen_vel = no pull= no -- 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.
