On 11/14/16 5:11 PM, Mohsen Ramezanpour wrote:
Dear Gromacs users,
I have made an initial system with a number of molecules in a "large" box.
Large means a box of size 50 50 50 nm?
I am interested in the self-assembly process of molecules (parametrized in
charmm36 ff) in the box.
I expected pressure coupling to shrink the box quickly, but it seems it
fails to do so. The simulation box did not change (ca. 0.5 nm in each
direction) which seems strange to me.
I have used four different P-couple schemes for 4 different type of
self-assemblies:
1) isotropic
pcoupl = berendsen
pcoupltype = isotropic
tau_p = 5.0
compressibility = 4.5e-5
ref_p = 1.0
2) semiisotropic
pcoupl = berendsen
pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
3) anisotropic with *fix shape* of box (*but the size could change*)
pcoupl = berendsen
pcoupltype = anisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
ref_p = 1.0 1.0 1.0 0 0 0
4) anisotropic with *both size and shape able to change*
pcoupl = berendsen
pcoupltype = anisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5
ref_p = 1.0 1.0 1.0 0 0 0
Here are some other parameters in mdp file which might be useful for
finding the problem:
integrator = md
dt = 0.002
nsteps = 50000
nstlog = 1000
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstcalcenergy = 100
nstenergy = 1000
cutoff-scheme = Verlet
nstlist = 20
rlist = 1.2
coulombtype = pme
rcoulomb = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
tcoupl = berendsen
tc_grps = Molecules water_ions
tau_t = 1.0 1.0
ref_t = 355 355
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
nstcomm = 100
comm_mode = linear
comm_grps = Molecules WI
You shouldn't reset COM motion like this.
refcoord_scaling = com
gen-vel = no
I can make the initial system smaller, but I think starting from a large
box would be better because it gives all the molecule enough freedom to
move and assemble in better way.
Is not it right to expect the p-couple shrink the box in nanoseconds? This
was only for 100 ps but I expected more shrinkage of box. What do you think?
100 ps is nothing.
If you have a box full of water, as your settings above imply, you can't expect
much of a change. Why do you need the box to shrink, or why do you expect it
to? A box will only shrink a lot if there is substantial void space, e.g.
intentional or due to a poor initial approximation of the system that requires
equilibration.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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