[gmx-users] md.mdp for CHARMM36

[Sajad Ahrari]

Hello Dears,
I am trying to do an all-atom simulation on a protein holding MG ions ans ATP as the hetero-atoms. in order to prepare my md.tpr, I used the md.mdp file which was prepared by Justin tutorial on "protein ligand". However I modified it according to the following lines (I mean I added lines 3, 4 and 7 and also changed my mdp according to other lines ). I have also prepared the new mdp file that I used to prepare my md.tpr file. Could you take a look and see if the mdp terms are reasonably changed.  

Best regards,Sajjad
Lines that were suggested to be modified while working with CHARMM (http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM):
 
1-constraints = h-bonds
2-cutoff-scheme = Verlet
3-vdwtype = cutoff
4-vdw-modifier = force-switch
5-rlist = 1.2
6-rvdw = 1.2
7-rvdw-switch = 1.0
8-coulombtype = PME
9-rcoulomb = 1.2
10-DispCorr = no

the modified mdp that I used to prepare md.tpr:

title       = Protein-ligand complex MD simulation 
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 500000    ; 2 * 500000 = 1000 ps (1 ns)
dt          = 0.002     ; 2 fs
; Output control
nstxout             = 0         ; suppress .trr output 
nstvout             = 0         ; suppress .trr output
nstenergy           = 1000      ; save energies every 2.0 ps
nstlog              = 1000      ; update log file every 2.0 ps
nstxout-compressed  = 1000      ; write .xtc trajectory every 2.0 ps
compressed-x-grps   = System
energygrps          = Protein ATP MG
; Bond parameters
continuation    = yes           ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints 
constraints     = h-bonds     ; all bonds (even heavy atom-H bonds) constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type         = grid      ; search neighboring grid cells
nstlist         = 10        ; 20 fs, largely irrelevant with Verlet
rcoulomb        = 1.2       ; short-range electrostatic cutoff (in nm)
rvdw            = 1.2       ; short-range van der Waals cutoff (in nm)
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
; Electrostatics
coulombtype     = PME       ; Particle Mesh Ewald for long-range electrostatics
pme_order       = 4         ; cubic interpolation
fourierspacing  = 0.16      ; grid spacing for FFT
; Temperature coupling
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc-grps     = Protein_ATP_MG Water_and_ions    ; two coupling groups - more accurate
tau_t       = 0.1   0.1                     ; time constant, in ps
ref_t       = 300   300                     ; reference temperature, one for each group, in K
; Pressure coupling 
pcoupl      = Parrinello-Rahman             ; pressure coupling is on for NPT
pcoupltype  = isotropic                     ; uniform scaling of box vectors
tau_p       = 2.0                           ; time constant, in ps
ref_p       = 1.0                           ; reference pressure, in bar
compressibility = 4.5e-5                    ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = no  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = no        ; assign velocities from Maxwell distribution