On 4/13/15 12:38 AM, Iris Nira Smith wrote:
Hello, I'm utilizing gromacs 4.6.3 to set up my md simulation to run a ligand-only invacuo (no water) system for 500 ps prior to running my protein-ligand complex to determine the stability of the ligand. I have successfully run an energy minimization with the em-invaco.mdp file below (in absence of periodicity and infinite cut-offs). When running the equilibration should it be broken up into 2 phases: phase 1-nvt, phase 2-npt or is nvt sufficient?
You can't do NPT in vacuo with an infinite system.
If so, should it also be done utilizing an implicit solvent model such as GBSA for both equilibration and production run (see also eqb-invacuo.mdp below)?
Implicit solvent and vacuum are physically different. If your in vacuo run is only to assess topological stability, don't bother with implicit solvent, because that adds a layer of complexity that will make it hard to tell if there are any problems. Implicit models are very approximate.
-Justin
em-invacuo.mdp ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm options ; steep = steepest descent minimization ; MD = Leap Frog algorith for integrating NewtonĊ equations of motion ) emtol = 10.0 ; Stop minimization when the Fmax < 10 kJ/mol/nm. emstep = 0.01 ; Energy step size nsteps = 10000 ; Maximum number of (minimization) steps to perform nstenergy = 10 ; Write energies to disk every nstenergy steps ; ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 0 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, grid) rlist = 0 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb = 0 ; long range electrostatic cut-off rvdw = 0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = no ; Periodic Boundary Conditions (yes/no) eqb-invacuo.mdp define = -DFLEXIBLE constraints = none ; Bond types to replace by constraints integrator = md ;Algorithm options dt = 0.002 ; timestep for integration nsteps = 50000 ; Maximum number of steps to perform 100 ps nstxout = 1000 ; frequency to write coordinates to output trajectory 2 ps nstfout = 1000 ; frequency to write forces to output trajectory 2 ps nstvout = 1000 ; frequency to write velocities to output trajectory 2 ps nstxtcout = 1000 nstlog = 1000 ; frequency to write energies to log 2 ps nstenergy = 1000 ; frequency to write energies to edr ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 0 ; Frequency to update the neighbor list and long range forces ns_type = simple rlist = 0 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic interactions vdwtype = cut-off rcoulomb = 0 ; long range electrostatic cut-off rvdw = 0 ; long range Van der Waals cut-off pbc = no ; Periodic Boundary Conditions (yes/no) epsilon_rf = 0 rgbradii = 0 comm_mode = angular comm-grps = system optimize_fft = yes ; ; V-rescale temperature coupling is on tcoupl = v-rescale tc-grps = system tau-t = 0.1 ref-t = 300 ; ; Pressure coupling is off Pcoupl = no ; ; Generate velocites is on gen_vel = yes gen_temp = 300 gen_seed = -1 ; ; Implicit solvent implicit_solvent = GBSA gb_algorithm = Still gb_epsilon_solvent = 80 sa_surface_tension = 2.25936 nstgbradii = 1 rgbradii = 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist sa_algorithm = Ace-approximation sa_surface_tension = -1 Best, Iris Nira Smith, Ph.D. Candidate Briggs Computational Biochemistry/Biophysics Laboratory University of Houston 402E Health Science Center Houston, TX 77204 A Carnegie-designated Tier One public research university Phone:281-726-0341 Email: irisnsm...@comcast.net connormichaellogsdon.blogspot.com
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
