Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
Sorry for the inconvenience about the .mdp file.
The mdp file used for the final run is
*_
final.mdp file_*_
_title = Protein in POPC bilayer
cpp = /usr/bin/cpp
constraints = all-bonds
constraint-algorithm= Lincs
integrator = md
dt = 0.002
nsteps = 5000
nstcomm = 1
nstxout = 50
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1
coulombtype = PME
rcoulomb = 1
vdw-type = Cut-off
rvdw = 1
; Berendsen temperature coupling is on in two groups
tcoupl = berendsen
tc_grps = Protein POPC SOL CL-
tau_t = 0.1 0.1 0.1 0.1
ref_t = 300 300 300 300
Don't couple ions seperately. See
http://wiki.gromacs.org/index.php/Thermostats
Mark
; Energy monitoring
energygrps = Protein POPC SOL CL-
; Pressure coupling is on
;Pcoupl = berendsen
tau_p = 2.0 2.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
Pcoupl_type = semiisotropic
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
_*
mdp file for position restraint mdrun*_
title = Protein in POPC bilayer
cpp = /usr/bin/cpp
define = -DPOSRES -DPOSRES_LIPID
constraints = all-bonds
constraint-algorithm= Lincs
integrator = md
dt = 0.002
nsteps = 5000
nstcomm = 1
nstxout = 50
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1
coulombtype = PME
rcoulomb = 1
vdw-type = Cut-off
rvdw = 1
; Berendsen temperature coupling is on in two groups
tcoupl = berendsen
tc_grps = Protein POPC SOL CL-
tau_t = 0.1 0.1 0.1 0.1
ref_t = 300 300 300 300
; Energy monitoring
energygrps = Protein POPC SOL CL-
; Pressure coupling is on
;Pcoupl = berendsen
tau_p = 2.0 2.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
Pcoupl_type = semiisotropic
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
Thanking you,
Yours sincerely,
Pawan
On Mon, Apr 6, 2009 at 5:35 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
1. Were there gaps between the water and lipid headgroups?
If so,
the lipids may be pulling towards the solvent. Restrain the
lipids
and run an equilibration for a longer time.
Gap was there when I used a value of 0.5 in the vdwradii.dat
file. The gap reduced as I decreased the value from 0.5 to 0.35
to the default of 0.15. I tried all the three possibilities.
When I used the default vdwradii.dat file and made the solvation
followed by simulation runs the lipids didnt pull apart. But
there were water molecules on the sides of the bilayer and not
in the interior.
This indicates to me that the gaps are causing the problem. Do not
run simulations with water in or around the lipids; it is not
realistic. You can clean up such a starting structure, either by
some clever script like those on the wiki, or by looking at the
structure, taking note of which water molecules are offending, and
deleting them manually from the coordinate file.
The other option is to temporarily give genbox a box that is
slightly smaller in the x-y dimensions, so that it will try to place
less water around the POPC periphery.
2. 5000 steps is far too short to expect any realistic
behavior for
lipids. Equilibration can take upwards of 10-20 ns.
As per your suggestion I have made the final mdrun now again
with 500000 steps. Hopefully this will work.
3. You haven't mentioned the contents of your .mdp file. Maybe
you're doing something wrong.
I am using the same .mdp file which I posted before. I have just
removed the restraints.
I don't have record of the previous email; as a general guide, post
the .mdp by default when experiencing weird behavior. That way the
users on this list won't have to go combing through the archive to
find it. If you want free help, make it easy to help you :)
-Justin
4. Are you using Gromos/Berger or OPLS/converted Berger for your
system? There have been so many of these questions from
different
users over the last few days that it's hard to keep track.
If you
are using OPLS/converted Berger you may have made a mistake in
translating the C6/C12 parameters.
I am using gromos 96 force field (G43a1) and as per your
suggestion I have edited the lipid.itp file to remove the part
containing " lipid-gromos interactions".
Thanking you,
Yours sincerely,
Pawan
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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