On 9/20/12 3:04 PM, Lara Bunte wrote:
Hello
Could you please take a look on my new pr.mdp file that I created for
equilibrating water around lumiflavin. grompp works but I guess there must be
something wrong because after grompp I am using mdrun and get this warning:
Warning: 1-4 interaction between 1 and 5 at distance 2.429 which is larger than
the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
step 1: Water molecule starting at atom 8655 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
My system is lumiflavin in a dodecahedron box, a tip3p water model and the
CHARMM27 force field. This is my pr.mdp file:
You are not using correct settings. Peter posted these the other day for
CHARMM27:
http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html
Beyond that, how successful was energy minimization? How did you derive the
topology? Does an in vacuo run of just the solute work, or does it fail as well
(implicates an incorrect topology)?
-Justin
title = Lumiflavin NVT equilibration
define = -DPOSRES
; Run parameters
integrator = md
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 = 1.2 ; short-range neighborlist cutoff (in nm)
rlistlong = 1.4
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; 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 = ISO 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 off
pcoupl = no ; no pressure coupling in NVT
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
Thanks for helping me
Best 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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