On 10/19/19 12:48 PM, Mahsa Rezaei wrote:
Dear gromacs users, I am using following pull code in md simulation for pulling a ligand across the plasma membrane model. My size box is 8.52807 8.52807 14.00000. And the pull distance is less than one-half the length of the box vector along.pull distance is 6 nm. when I execute this command,I got warning: gmx grompp -f md_pull.mdp -c complex.gro -p topol.top -r complex.gro -n index.ndx -o pull.tpr WARNING 1 [file md_pull.mdp]: Pull group 1 has atoms at a distance larger than 0.9 times half the box size from the PBC atom (27119). If atoms are or will more beyond half the box size from the PBC atom, the COM will be ill defined. Pull group natoms pbc atom distance at start reference at t=0 1 54231 27120 2 4 2 -3.769 nm -3.769 nm Estimate for the relative computational load of the PME mesh part: 0.10 This run will generate roughly 1238 Mb of data Fatal error: Too many warnings (1). If you are sure all warnings are harmless, use the -maxwarn option. What should I do? I would be very appreciated for your such kind helps.
The reference for determining periodic distances is simply the numerical middle of the atom selection, which may not have any resemblance to the geometric center. If your group(s) is(are) non-spherical in nature, you need to select an appropriate atom for grompp and mdrun to compute the periodic distances.
-Justin
My mdp file : integrator = md dt = 0.002 nsteps = 290000 ; 580 ps ; Output parameters nstlog = 1000 nstxout = 500 ; every 1 ps nstvout = 500 nstfout = 500 nstxtcout = 500 ; every 1 ps nstcalcenergy = 500 nstenergy = 500 cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw_switch = 1.0 rvdw = 1.2 ; tcoupl = Nose-Hoover tc_grps = PROT MEMB_LIG SOL_ION tau_t = 1.0 1.0 1.0 ref_t = 303.15 303.15 303.15 ; pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm = LINCS continuation = yes ; nstcomm = 100 comm_mode = linear comm_grps = PROT MEMB_LIG SOL_ION ; refcoord_scaling = com ; Pull code pull = yes pull_ncoords = 1 ; only one reaction coordinate pull_ngroups = 2 pull_group1_name = BILAYER pull_group2_name = LIG pull_coord1_type = umbrella ; harmonic potential pull_coord1_geometry = direction pull_coord1_vec = 0.0 0.0 1.0 pull_coord1_groups = 1 2 pull_coord1_start = yes ; define initial COM distance > 0 pull_coord1_rate = 0.01 ; 0.01 nm per ps =10nm per ns pull_coord1_k = 2000 ; kJ mol^-1 nm^-2 pull_nstxout = 500 ; every 1 ps pull_nstfout = 500 ; every 1 ps [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&> 10/19/19, 08:14:02 PM
-- ================================================== 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.