[gmx-users] parameters of em.mdp

[ahmet yıldırım]

Dear users,

I am using the Reaction-Field method for electrostatics interactions.
I used the
following parameters for all input files (em.mdp, pr.mdp, nvt.mdp, npt.mdp,
md.mdp). I just changed as an epsilon_rf=78 in md.mdp. If I set
nstlist=rlist=rcoulomb=rvdw=1.0 for energy minimization, would not it be
better? What is your suggestions?

; Neighbor Searching Parameters
nstlist                 = 5
ns-type                 = Grid
pbc                = xyz
rlist                   = 0.9
; Electrostatics
coulombtype             = Reaction-Field
rcoulomb                = 1.4
epsilon_rf              = 54
; VdW
vdw-type                = Cut-off
rvdw                    = 1.4
*
Another question:* I used 200 K (in pr.mdp) and 300 K (in nvt.mdp, npt.mdp
and md.mdp) the reference temperature for coupling. I analysed the
temperature after production run. I get "Temperature=312.646" (g_energy -f
md.edr -o temperature.xvg). that is, The temperature has increased
(approximately
12 K) during the simulation. What could be the reason for the increase in
temperature? I had setted to 200 K the reference temperature for coupling
in pr.mdp. it can cause?

My em.mdp file is as the following:
*em.mdp:*
title                = Energy Minimization ; Title of run
cpp                = /lib/cpp         ; Preprocessor: Line tell the program
the standard locations where to find certain files
define                  = -DFLEXIBLE          ; defines to pass to the
preprocessor

; Run Control
integrator            = steep        ; steep integrator (steep = steepest
descent minimization)
nsteps                = 2500        ; maximum number of steps to integrate

; Energy Minimization
emtol                = 1000.0         ; [kJ/mol/nm] minimization is
converged when max force is < emtol
emstep                  = 0.01               ; [nm] initial step-size

; Output Control
nstxout                 = 0             ; [steps] freq to write coordinates
to trajectory
nstvout                 = 0             ; [steps] freq to write velocities
to trajectory
nstfout                 = 0             ; [steps] freq to write forces to
trajectory
nstlog                  = 1             ; [steps] freq to write energies to
log file
nstenergy            = 1        ; [steps] freq to write energies to energy
file
energygrps            = System    ; group(s) to write to energy file

; Neighbor Searching Parameters
nstlist                 = 5                 ; [steps] freq to update
neighbor list
ns-type                 = Grid              ; method of updating neighbor
list
pbc                = xyz                ; periodic boundary conditions
(yes/no)in all directions
rlist                   = 0.9               ; [nm] cut-off distance for the
short-range neighbor list

; Electrostatics
coulombtype             = Reaction-Field  ; Reaction-Field electrostatics
rcoulomb                = 1.4             ; [nm] distance for Coulomb
cut-off
epsilon_rf              = 54              ; The relative dielectric
constant of the reaction field

; VdW
vdw-type                = Cut-off           ; twin-range cut-off with rlist
where rvdw >= rlist
rvdw                    = 1.4               ; [nm] distance for LJ cut-off

; Bonds
constraints             = none         ; convert all bonds to constraints

-- 
Ahmet Yıldırım
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120323/628283e1/attachment.html>