[gmx-users] mdp option for implicit solvent simulation

[Justin Lemkul]

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 <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?
>>

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

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