On 4/23/20 3:01 PM, lazaro monteserin wrote:
I am trying to run a temperature equilibration of my system and I get the following error: ======================= NOTE 1 [file nvt.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file nvt.mdp]: Center of mass removal not necessary for Andersen. All velocities of coupled groups are rerandomized periodically, so flying ice cube errors will not occur. ERROR 1 [file nvt.mdp]: nstcomm must be 1, not 100 for Andersen, as velocities of atoms in coupled groups are randomized every time step ======================= but I don't even have in my nvt.mdp any values for the nstcomm or restriction of center of masses translations or rotation. So I honestly do not know what is happening here. Do anybody have an idea of what is going on?
For any settings no explicitly listed, the defaults are used. See the manual:
http://manual.gromacs.org/current/user-guide/mdp-options.html -Justin
This are the parameters for my cvt.mdp: ====================================================== define = -DPOSRES ; position restrain for waters ; Run parameters integrator = md-vv ; velocity Verlet algorithm nsteps = 50000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 1 fs, largely irrelevant with Verlet rcoulomb = 333.3 ; short-range electrostatic cutoff (in nm) rvdw = 333.3 ; short-range van der Waals cutoff (in nm) DispCorr = EnerPres ; account for cut-off vdW scheme ; Electrostatics coulombtype = cutoff ; cutoff treatment ; Temperature coupling is on tcoupl = andersen ; Andersen thermostat tc-grps = System ; couple system to bath tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K nstcomm = 1 ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ===================================================================== Kindly, Lazaro
-- ================================================== 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.
