On 3/24/14, 7:57 AM, Ankita Naithani wrote:
Hi, so I modified my mdp file which now looks like the following: title = production MD ; Run parameters integrator = md ; leap-frog algorithm ;nsteps = 20000000 ; 0.005 * 20000000 = 100000 ps or 100 ns ;nsteps = 200000 ; 0.005 * 200000 = 1 ns ;dt = 0.005 ; 5 fs nsteps = 33333333 ; 0.003 * 33333333 = 100000 ps or 100 n dt = 0.003 ; 3 fs ; Output control nstxout = 0 ; save coordinates every 2 ps nstvout = 0 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 5 ps nstenergy = 1000 ; save energies every 5 ps nstlog = 1000 ; update log file every 5 ps ; Bond parameters constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 25 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) rlistlong = 1.0 ; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT nstcomm = 10 ; remove com every 10 steps ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 318 318 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = berendsen ; Berendsen thermostat pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 1.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; Velocity generation is on gen_temp = 318 ; reference temperature, for protein in K -------------------------------------------------- But, when I try to generate the tpr file on the cluster itself using gromacs 4.6.3, I get the following error: NOTE 1 [file md3.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file md3.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy Generated 3403 of the 3403 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3403 of the 3403 1-4 parameter combinations Segmentation fault Can anyone please suggest further?
Do as the notes suggest. They're not fatal errors, they're just cautionary. You should probably educate yourself a bit further on what all of these algorithms are by taking a look at http://www.gromacs.org/Documentation/Cut-off_schemes. The Verlet scheme is not mandatory, but it is required by the type of parallelization you requested.
Reviewers may question the changes in version and cutoff methods when critiquing your work, so be aware of that. Also, the instability you are seeing is probably a result of the large time step, unless you are using virtual sites.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
