<div class="gmail_quote"><span dir="ltr"></span>Hello gmx users,<br><br>My system for NVT equilbration runs into segmentation fault as soon as I try to run it.<br>It does not give any warning or hint of what might be going wrong.<br>
Since I am a new user I am having difficulty exploring the plausible reasons.<br>
<br>System: Protein( polyhistidine), 20 2,5-dihydroxybenzoic acid anions,
1:1 water: methanol (~3000 molecules of each) in 8 nm cube<br><br><br>
I had had EM of the system using steepest decent. Outcome:<br><br>Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1000.<br>Potential Energy = 1.5354981e+19<br>Maximum force = inf on atom 651<br>
Norm of force = inf<br><br><b>The minim.mdp </b>is:<br>; minim.mdp - used as input into grompp to generate em.tpr<br>; Parameters describing what to do, when to stop and what to save<br>integrator = steep ; Algorithm (steep = steepest descent minimization)<br>
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm<br>emstep = 0.02 ; Energy step size<br>nsteps = 50000 ; Maximum number of (minimization) steps to perform<br>
<br>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>nstlist = 1 ; Frequency to update the neighbor list and long range forces<br>ns_type = grid ; Method to determine neighbor list (simple, grid)<br>
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)<br>coulombtype = PME ; Treatment of long range electrostatic interactions<br>rcoulomb = 1.0 ; Short-range electrostatic cut-off<br>rvdw = 1.0 ; Short-range Van der Waals cut-off<br>
pbc = xyz ; Periodic Boundary Conditions (yes/no)<br>constraints = none<br><br><br><br><br><b>The nvt.mdp</b>:<br><br>title = hist NVT equilibration<br>
define = -DPOSRES ; position restrain the protein<br>; Run parameters<br>integrator = md ; leap-frog integrator<br>nsteps = 50000 ; 2 * 50000 = 100 ps<br>dt = 0.002 ; 2 fs<br>; Output control<br>
nstxout = 100 ; save coordinates every 0.2 ps<br>nstvout = 100 ; save velocities every 0.2 ps<br>nstenergy = 100 ; save energies every 0.2 ps<br>nstlog = 100 ; update log file every 0.2 ps<br>; Bond parameters<br>
continuation = no ; first dynamics run<br>constraint_algorithm = lincs ; holonomic constraints<br>constraints = none ;<br>lincs_iter = 1 ; accuracy of LINCS<br>lincs_order = 4 ; also related to accuracy<br>
; Neighborsearching<br>ns_type = grid ; search neighboring grid cells<br>nstlist = 5 ; 10 fs<br>rlist = 1.0 ; short-range neighborlist cutoff (in nm)<br>rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)<br>
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)<br>; Electrostatics<br>coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics<br>pme_order = 4 ; cubic interpolation<br>fourierspacing = 0.16 ; grid spacing for FFT<br>
; Temperature coupling is on<br>tcoupl = V-rescale ; modified Berendsen thermostat<br>tc-grps = Protein Non-Protein ; two coupling groups - more accurate<br>tau_t = 0.1 0.1 ; time constant, in ps<br>ref_t = 300 300 ; reference temperature, one for each group, in K<br>
; Pressure coupling is off<br>pcoupl = no ; no pressure coupling in NVT<br>; Periodic boundary conditions<br>pbc = xyz ; 3-D PBC<br>; Dispersion correction<br>DispCorr = EnerPres ; account for cut-off vdW scheme<br>
; Velocity generation<br>gen_vel = yes ; assign velocities from Maxwell distribution<br>gen_temp = 300 ; temperature for Maxwell distribution<br>gen_seed = -1 ; generate a random seed<br><br><br>I tried to decrease the step size, that also runs into seg fault error.<br>
<br><br>Kindly guide.<br><br>Thanks,<br><font color="#888888">SN<br>
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