[gmx-users] Implicit solvent tutorial

[Justin A. Lemkul]

lina wrote:
> 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.
> 

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
>> _________________________________________________________
>> 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

-- 
========================================

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

========================================