[gmx-users] mdp option for implicit solvent simulation

[Sanku M]

Hi Erik,
  That statement was a typo. The simulation will be done in implicit solvent ( not in gas phase).
Sanku


________________________________
 From: Erik Marklund <erikm at xray.bmc.uu.se>
To: Sanku M <msanku65 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, January 11, 2013 5:04 AM
Subject: Re: [gmx-users] mdp option for  implicit solvent simulation
 
Hi,

If you're simulating in the gas-phase, how come you want implicit solvent?

Erik

On Jan 11, 2013, at 5:07 AM, Sanku M wrote:

> Hi,
>   I am trying to do implicit solvent simulation for a protein in gas-phase. I have a few questions :
> 1) should I use sd integrator?
> 
> 2) should I also use no periodic condition considering continuum dielectric ?
> 
> 3) in the JCTC 2010 paper by Lindahl and co-worker, it is mentioned that no cutoffs were used for implicit solvent simulations.
>  But, again in implicit solvent setup the rgblist should be equal to rlist.
> Now, if I use rlist=0 ( as all interactions are considered), should I also make rgblist=0?
> Does it mean the setup was following type: i.e.
> 
>   ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist                  = 0
> ; ns algorithm (simple or grid)
> ns-type                  = simple
> ; Periodic boundary conditions: xyz, no, xy
> pbc                      = no
> periodic_molecules       = no
> ; nblist cut-off
> rlist                    = 0
> ; long-range cut-off for switched potentials
> rlistlong                = -1
> 
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype              = cut-off
> rcoulomb-switch          = 0
> rcoulomb                 = 0
> ; Relative dielectric constant for the medium and the reaction field
> epsilon_r                = 1
> epsilon_rf               = 1
> ; Method for doing Van der Waals
> ; Method for doing Van der Waals
> vdw-type                 = Cut-off
> ; cut-off lengths
> rvdw-switch              = 0
> rvdw                     = 0
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr                 = No
> 
> 
> ; IMPLICIT SOLVENT ALGORITHM
> implicit_solvent         = GBSA
> 
> ; GENERALIZED BORN ELECTROSTATICS
> ; Algorithm for calculating Born radii
> gb_algorithm             = Still
> ; Frequency of calculating the Born radii inside rlist
> nstgbradii               = 1
> ; Cutoff for Born radii calculation; the contribution from atoms
> ; between rlist and rgbradii is updated every nstlist steps
> rgbradii                 = 0
> ; Dielectric coefficient of the implicit solvent
> gb_epsilon_solvent       = 80
> ; Salt concentration in M for Generalized Born models
> gb_saltconc              = 0.150
> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
> gb_obc_alpha             = 1
> gb_obc_beta              = 0.8
> gb_obc_gamma             = 4.85
> gb_dielectric_offset     = 0.009
> sa_algorithm             = Ace-approximation
> sa_surface_tension       = -1
> 
> 
> 
> Some idea about the implicit solvent setup will be appreciated.
> Sanku
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