[gmx-users] Implicit solvent tutorial

[lina]

On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni
<gianluca.santoni at 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.

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
> _________________________________________________________
> Please avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
>
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists