On 1/11/13 9:34 AM, Sanku M wrote:
Hi Erik,
That statement was a typo. The simulation will be done in implicit solvent (
not in gas phase).
Sanku
________________________________
From: Erik Marklund <er...@xray.bmc.uu.se>
To: Sanku M <msank...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@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?
Probably, since you are likely dealing with relatively few degrees of freedom.
2) should I also use no periodic condition considering continuum dielectric ?
Correct.
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?
Yes.
Most of these ideas have been discussed numerous times in the list archive.
-Justin
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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--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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