On 6/29/12 6:01 AM, Lara Bunte wrote:
Hello
I use a CHARMM27 force field and my system is lumiflavin in water. I use the
spc216 water model, a dodecahedral box with 1.3 nm. I want to make a
CHARMM27 should be combined with TIP3P, not SPC.
structure minimization. I made a file pr.mdp. Could you please tell me, what
I could do better in this file, or what is wrong? I guess there has to be
something wrong, because GROMACS failed with grompp -f pr.mdp -p topol.top -c
em.gro -o pr.tpr with the error: "Water molecule starting at atom 3924 can
not be settled. Check for bad contacts and/or reduce the timestep if
appropriate. "
My pr.mdp file is:
Your problem is that you're trying to run position-restrained MD, not energy
minimization. Consult any tutorial for a more appropriate EM file. Without
adequate EM, any simulation with almost certainly crash.
-Justin
title = lumiflavin NPT 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 = 5000 ; save coordinates every 4
ps nstvout = 5000 ; save velocities every 4 ps nstenergy
= 5000 ; save energies every 4 ps nstlog = 5000 ;
update log file every 4 ps
; Bond parameters continuation = yes ; Restarting after NVT
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 = 10 ; edited to 1 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 = 0.12 ; grid spacing for FFT
; Temperature coupling is on tcoupl = V-rescale ; modified
Berendsen thermostat tc-grps = Isoalloxazin Sol ; two coupling
groups - more accurate tau_t = 0.1 0.1 ; time constant, in
ps ref_t = 300 300 ; reference temperature, one for each
group, in K
; Pressure coupling is on pcoupl = berendsen ; Pressure coupling
on in NPT pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps ref_p = 1.0
; reference pressure, in bar compressibility = 4.5e-5 ; isothermal
compressibility of water, bar^-1 refcoord_scaling = all
; Velocity generation gen_vel = yes ; assign velocities from
Maxwell distribution gen_temp = 300 ; temperature for Maxwell
distribution gen_seed = -1 ; generate a random seed
Thank you for helping me Greetings Lara
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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