On 2010-12-22 22.57, Sanku M wrote:
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 ?
yes.
you would just exchange PME for RF. That's all. There is an enormous of
literature about this, an our paper is one which shows that at least for
our examples, but I would like to a argue for any system with full
charges (rather than just dipoles like water), PME is much better than
anything else.
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 <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*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 <[email protected] <mailto:[email protected]>>
> *To:* [email protected] <mailto:[email protected]>
> *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.
[email protected] <mailto:[email protected]>http://folding.bmc.uu.se
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
--
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