Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private tutor. I am CC'ing the list and ask that further comments and
questions will be posted there.
On 2/25/13 7:42 AM, mrda...@gmail.com wrote:
Dear Justin
Greetings
I simulate HIV-1 Protease with its substrate for 20ns in cubic box filled with
SPC water using the following parameters:
title = n.pdb
cpp = /lib/cpp
constraints = none
integrator = md
dt = 0.001
nsteps = 20000000
nstcomm = 1
comm_mode = Linear
comm_grps =
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 100
nstenergy = 100
nstlist = 10
ns_type = grid
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in three groups
Tcoupl = berendsen
tau_t = 0.1
tc-grps = system
ref_t = 310
; Pressure coupling is on
Pcoupl = berendsen
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 310 K.
gen_vel = yes
gen_temp = 310.0
gen_seed = 173529
Unfortunately the dimer is dissociate to its monomers. what is the problem
causing this unwanted event?
thank you very much for your considerations
I doubt it's actually dissociating. What you're seeing is probably a simple
result of periodic boundary conditions.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
If a trajectory that has been properly post-processed by trjconv shows a
dissociation event, then you should be able to easily observe why it happens by
watching the trajectory in your favorite visualization software.
-Justin
--
========================================
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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