shivangi nangia wrote:
Hello gmx-users,
I have a 5 ang box with equal number of water and methanol molecules
(1800), a neutral peptide, 8 hydroxide ions and 10 Li+ ions. The system
is overall +2 charged.
If your box truly is 5 A (0.5 nm), grompp should have failed based on your
cutoffs. I assume you have a 5-nm box?
I am trying to to do a NVT equilibration which runs into the following
error:
t = 0.000 ps: Water molecule starting at atom 11816 can not be settled.
Check for bad contacts and/or reduce the timestep.
Did you do energy minimization first? If so, what was the outcome? Were the
energies and forces acceptable? What force field are you using? The generic
information about your problem can be found at:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
-Justin
the nvt.mdp is:
title = hist NVT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = no ; first dynamics run
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 ; 10 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)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; 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 = 250 250 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 250 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
I did try to reduce the timestep from 2 fs to 1 fs but ran into the same
error.
Searching through a few archives I got a hint it is something do to with
water's density per cubic nm.
Is that whats going on here?
If yes, then how do I randomly delete some water molecules from my system?
Please help.
Thanks,
Shivangi
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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