On 1/17/13 12:15 PM, fatemeh ramezani wrote:
1. For separate equilibration of AU and Protein, I'm using this em.mdp file for
equilibration in step 1, that Protein and SOL are frozen:
This is not an equilibration, this is an energy minimization, which will likely
not accomplish much with so many particles frozen.
title = n.pdb
cpp = /lib/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.002
nsteps = 40000
;constraint_algorithm = shake
;shake_tol = 0.0001
;nstenergy = 10
;nstxtcout = 10
;nstlist = 5
ns_type = grid
rlist = 1
coulombtype = PME
rcoulomb = 1
rvdw = 1.2
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Energy minimizing stuff
emtol = 1000.0
emstep = 0.01
freezegrps = Protein SOL
freezedim = Y Y Y Y Y Y
comm_mode = None
I suppose this .mdp file will allow whatever the Au particle is to move, but I
don't see much point to running anything where the solvent is frozen. Freezing
water also makes -DFLEXBILE irrelevant.
2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain:
title = n.pdb
cpp = /lib/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.002
nsteps = 40000
;constraint_algorithm = shake
;shake_tol = 0.0001
;nstenergy = 10
;nstxtcout = 10
;nstlist = 5
ns_type = grid
rlist = 1
coulombtype = PME
rcoulomb = 1
rvdw = 1.2
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Energy minimizing stuff
emtol = 1000.0
emstep = 0.01
freezegrps = AU AUI AUC
freezedim = Y Y Y Y Y Y Y Y Y
comm_mode = None
3. In simulation, I'm using this md.mdp file:
title = Yo
cpp = /lib/cpp
define =
integrator = md
tinit = 0.00000
dt = 0.002
nsteps = 250000
nstxout = 2500
nstvout = 2500
nstlog = 500
nstenergy = 250
nstxtcout = 0
pbc = xyz
rlist = 1.00
coulombtype = PME
r_coulomb = 1.00
The correct keyword is "rcoulomb."
fourierspacing = 0.10
Why switch the fourierspacing here? You used 0.12 before, and now you'r eusing
0.10.
pme_order = 6
ewald_rtol = 1e-6
vdw-type = switch
rvdw-switch = 0.90
rvdw = 1.00
These vdw settings are all very different from the previous minimization step.
It's usually a good idea to keep the settings the same throughout all steps,
otherwise you're using some broken form of a force field intermittently.
tcoupl = nose-hoover
tc_grps = SOL AUS AUB AUI
tau_t = 0.1 0.1 0.1 0.1
ref_t = 300 300 300 300
Depending on the size of these groups, assigning them to separate thermostats
may not be appropriate, and it doesn't appear that the protein is coupled
anywhere. Consult http://www.gromacs.org/Documentation/Terminology/Thermostats
Pcoupl = no
gen_vel = yes
gen_temp = 10
gen_seed = 173529
; GolP has been tested with lincs only
Then why turn off constraints?
constraints = none
constraint_algorithm = lincs
lincs_order = 4
lincs_iter = 1
lincs_warnangle = 80
freezegrps = AU AUI
freezedim = Y Y Y Y Y Y
comm_mode = None
Are these .mdp file right?
No. See points above. I can't comment on whether any of the settings are
correct for use with the GolP force field, but there are numerous
inconsistencies from a generic standpoint.
-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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
