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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