[gmx-users] Correct .mdp file for Amber99SB-ILDN ff implementation in Gromacs

[Mohsen Ramezanpour]

Dear Gromacs-users,

I am interested in simulation of protein-ligand system.

To do so, I have chosen the amber99sb-ildn force field.

Reading through the original paper on this force filed by D.E.Shaw group
(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/) I have made the
following equilibriu,.mdp and production-run.mdp files. I am not sure of
it, though. Please correct me if I am wrong.

The authors have used Desmond package not Gromacs for their simulations.
I was wondering if I should modify any terms because of using Gromacs
package?
(This is the case for using charmm force field in Gromacs).

I read other posts in gromacs list but I could not get any clear answer for
this.

Thanks in advance for your comments
Cheers
Mohsen


for Equilibrium.mdp, I made:

define                   =

; RUN CONTROL PARAMETERS
integrator               = md         ;
tinit                       = 0            ;
dt                          = 0.001     ; 1 femtosecond time step for
integration
nsteps                   = 500000   ; 1 ns

; OUTPUT CONTROL OPTIONS
nstxout                  = 0          ; Writing full precision coordinates
nstvout                  = 0          ; Writing velocities
nstfout                   = 0          ; writing forces
nstlog                    = 2500     ; Writing to the log file
nstenergy               = 2500    ; Writing out energy information
nstxtcout                = 2500    ; Writing coordinates every 5 ps
energygrps             = Protein   ligand  Water_and_ions
xtc_precision          = 1000
xtc-grps                 = System

; NEIGHBORSEARCHING PARAMETERS
nstlist                  = 10
ns-type                = Grid
pbc                      = xyz
rlist                      = 1.05
cutoff-scheme       = Verlet
nstcalclr                = 1

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype          = PME
rcoulomb               = 1.0
fourierspacing        = 0.1
vdw-type               = cut-off
rvdw                     = 1.0
optimize_fft           = yes
fourierspacing           = 0
fourier-nx               = 32
fourier-ny               = 32
fourier-nz               = 32
pme-order                = 4

; Temperature coupling
Tcoupl                   = v-rescale            ; in the original paper it
is Nose-Hoover thermostat
tc-grps                   = Protein_ligand  Water_and_ions
tau_t                      = 1.0      1.0
ref_t                       = 310      310

; Pressure coupling
Pcoupl                   = nose-hoover
Pcoupltype             = isotropic
tau_p                     = 5.5
compressibility       = 4.5e-5
ref_p                     = 1.00
refcoord_scaling      = com

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                    = yes    ; Assign velocities to particles by
taking them randomly from a Maxwell distribution
gen_temp                 = 50.0  ; Temperature to generate corresponding
Maxwell distribution
gen_seed                 = 1235   ; Seed for (semi) random number
generation.

; OPTIONS FOR BONDS
constraint-algorithm     = SHAKE
constraints                  = h-bonds


and for production-run.mdp, I just change the

dt                               = 0.002     ; 1 femtosecond time step for
integration
constraint-algorithm     = LINCS
constraints                  = all-bonds
gen_vel                       = no





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