[gmx-users] PME or Reaction field suitable for Gromos forcefield ?

[Sanku M]

Thanks David for the response. I was going through the supporting material of 
your paper to understand the methodology .
For G96 forcefield, you wrote
'For the gromos96 simulations marked “cutoff ” a reaction field with 
ǫ = 54 was applied beyond a cutoff of14 Å, for the opls/aa “cutoff ” simulations 
a straight cut-off 
of14 Å was chosen, and for the charmm “cutoff ” simulations a shift function was 
used between 
10 and 12 Å. In addition, simulations were carried out using Particle Mesh Ewald 
(PME) for the 
calculation of electrostatic interactions[10, 11].'

I am wondering what does the statement ' marked cutoff a reaction field with 
epsilon 54 beyond a cutoff of 14 Angstrom'  in terms of gromacs .mdp terminology 
?    Does it mean that you used reaction field as long range electrostatics for 
 G96.  But, I may have understood wrong because in the last line you again write, 
all simulations used 'PME'..  Does it mean that for G96 , the simulations were 
repeated with both reaction field and PME separately ?
For the reaction field, I have never used it before, so I was wondering if you 
can provide bit more details in 'mdout.mdp' terminolgy for general setup of 
simulation using  G96 forcefield . 
For example, for my simulation using Gromos96, I was using following mdout.mdp 
using PME.  I am not sure that is a suitable setup for gromos simulation or not . 
 Also, if I wanted to use reaction field, what modification I should have made 
here in long-range electrostat part ?



; RUN CONTROL PARAMETERS
integrator               = md
; Start time and timestep in ps
tinit                    = 0.0
dt                       = 0.004
nsteps                   = 40000000
; For exact run continuation or redoing part of a run
init_step                = 0
; mode for center of mass motion removal
comm-mode                = Linear
; number of steps for center of mass motion removal
nstcomm                  = 1
; group(s) for center of mass motion removal
comm-grps                =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 10
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc                      = xyz
; nblist cut-off
rlist                    = 1.4
domain-decomposition     = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = pme
rcoulomb-switch          = 0
rcoulomb                 = 1.4
; Relative dielectric constant for the medium and the reaction field
epsilon_r                = 1
epsilon_rf               = 1
; Method for doing Van der Waals
vdw-type                 = cut-off
; cut-off lengths
;rvdw-switch              = 0.7
rvdw                     = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = no
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1
; Seperate tables between energy group pairs
energygrp_table          =
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters
pme_order                = 6
ewald_rtol               = 1e-6
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no





________________________________
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wed, December 22, 2010 2:31:35 PM
Subject: Re: [gmx-users] PME or Reaction field suitable for Gromos forcefield ?

On 2010-12-22 21.57, Sanku M wrote:
>
>
> ------------------------------------------------------------------------
> *From:* Sanku M <msanku65 at yahoo.com>
> *To:* gmx-user at gromacs.org
> *Sent:* Wed, December 22, 2010 1:06:09 PM
> *Subject:* PME of Reaction field for Gromos forcefield ?
>
> Hi,
> I was trying to use g53a5 gromos forcefield for my study of protein in
> water . But, I found the original parameterization paper of gromos , in
> general uses reaction field for considering long range electrostatics .
> But, I was wondering among PME and reaction field , which one will be
> more apprpriate . Does PME cause any artifact if used with Gromos
> forcefield ?
> Alternatively, if I can get a sample .mdp file for typical gromos
> forcefield simulation, that will also be very helpful .
> Sanku
>
>
>
Check out
Oliver Lange, David van der Spoel and Bert de Groot: Scrutinizing 
Molecular Mechanics Force Fields on the Microsecond Timescale With NMR 
Data Biophys. J. 99 pp. 647-655 (2010)

We find that all FF perform better with PME.



-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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