lina wrote:
On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni
<gianluca.sant...@ibs.fr> wrote:
Hi gmx_users,
is there any tutorial for implicit solvent simulation available?
Hi,
I tried it few days ago.
1] pdb2gmx the water model choose none.
2] after editconf, go to energy minimization directly
* It's important to relax the system well.
3] NVT
4] You may find one .mdp file from gromacs-gpubench-dhfr.tar.gz
At bottom also attached the one I tried.
If some part is wrong, please let me know.
You should not use PBC. Cutoffs should be infinite (i.e. all set to zero). I
have never achieved stable simulations with finite cutoffs, even long ones, in
implicit solvent simulations.
The tcoupl setting is ignored when using the sd integrator, and there is very
little need to do any position restraining in implicit solvent simulations, as
there is no solvent to relax, you're just restraining the protein and not
accomplishing anything. gen_vel should be set to "yes" to generate velocities
following EM.
-Justin
Thanks,
define = -DPOSRES
integrator = sd
nsteps = 1000000000
dt = 0.0005
nstxout = 1000
nstvout = 1000
nstxtcout = 1000
nstenergy = 1000
nstlog = 1000
continuation = yes
constraints = all-bonds
ns_type = grid
nstlist = 1.0
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
coulombtype = Cut-off
pme_order = 4
fourierspacing = 0.16
tcoupl = V-rescale
tc-grps = A B C
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
pbc = xyz
gen_vel = no
ld_seed = -1
implicit_solvent = GBSA
gb_algorithm = OBC
nstgbradii = 1.0
rgbradii = 1.0
gb_epsilon_solvent = 80
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
sa_surface_tension = 0.0054
Thanks!
--
Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Grenoble
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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