[gmx-users] using charmm36 force field with gromacs

[Krzysztof Kuczera]

You can get a CHARMM36-compatible .mdp file if you build your system 
with CHARMM-GUI
(www.charmm-gui.org) and ask for GROMACS inputs to be generated

Krzysztof

On 11/3/15 3:32 PM, Yoav Atsmon-Raz wrote:
> Hi there,
>
> I'm a noob with Gromacs 4.6.7 which is interested in doing all-atom simulations with the charmm36 force field for a protein-membrane system while applying the Verlet cutoff  scheme. Basically I have two questions regarding this matter:
> 1) Does using the CHARMM36 ff necessitates any special modifications to the mdp files (minimization,equilibration,prod. run)?
> 2) Besides the "cutoff-scheme=verlet" line in the mdp files, do I need to add anything else?
>
> This is my prod. run mdp file:
>
> ; Run parameters
> integrator    = md        ; leap-frog integrator
> nsteps        = 50        ; 2 * 500000 = 1000 ps (1 ns)
> dt            = 0.002        ; 2 fs
> ; Output control
> nstxout        = 10        ; save coordinates every 2 ps
> nstvout        = 10        ; save velocities every 2 ps
> nstxtcout    = 10        ; xtc compressed trajectory output every 2 ps
> nstenergy    = 10    ; save energies every 2 ps
> nstlog        = 10        ; update log file every 2 ps
> ; Bond parameters
> continuation    = yes            ; Restarting after NPT
> constraint_algorithm = lincs    ; holonomic constraints
> constraints    = all-bonds            ; all bonds (even heavy atom-H bonds) constrained
> lincs_iter    = 1                    ; accuracy of LINCS
> lincs_order    = 4                    ; also related to accuracy
> ; Neighborsearching
> ns_type        = grid        ; search neighboring grid cels
> nstlist        = 5            ; 10 fs
> rlist        = 1.2        ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 1.2        ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.2        ; short-range van der Waals cutoff (in nm)
> cutoff-scheme   = Verlet
> ; Electrostatics
> coulombtype    = PME        ; Particle Mesh Ewald for long-range electrostatics
> pme_order    = 4            ; cubic interpolation
> fourierspacing    = 0.16        ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl        = Nose-Hoover            ; More accurate thermostat
> tc-grps        = POPC_Protein Water            ; two coupling groups - more accurate
> tau_t        = 0.5    0.5                ; time constant, in ps
> ref_t        = 323     323                ; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl        = Parrinello-Rahman        ; Pressure coupling on in NPT
> pcoupltype    = semiisotropic            ; uniform scaling of x-y box vectors, independent z
> tau_p        = 2.0                    ; time constant, in ps
> ref_p        = 1.0    1.0                ; reference pressure, x-y, z (in bar)
> compressibility = 4.5e-5    4.5e-5    ; isothermal compressibility, bar^-1
> ; Periodic boundary conditions
> pbc            = xyz        ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel        = no        ; Velocity generation is off
> ; COM motion removal
> ; These options remove motion of the protein/bilayer relative to the solvent/ions
> nstcomm         = 1
> comm-mode       = Linear
> comm-grps       = POPC_Protein Water
>
>
> Thanks in advance to anyone answering this!


-- 
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
1251 Wescoe Hall Drive, 5090 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html