[gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field

[Justin Lemkul]

On 11/29/15 7:35 PM, Rakesh Ramachandran wrote:
> Dear all,
>
>       I am using Gromacs 5.1 with CHARMM27 force field for protein
> simulation and using the following mdp options. I am really confused
> whether to use PME-switch option or only PME and what is the basic
> difference. Moreover for CHARMM I see switching needs to be performed, but
> with Verlet cutoff should I use Potential-switch, Force-switch
> or potential-shift-verlet. Also let me know if any other options need to be
> changed.
>
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist = 40
>
> ; ns algorithm (simple or grid)
> ns_type = grid ; search neighboring grid cells
>
> ; Periodic boundary conditions: xyz, no, xy
> pbc                 = xyz ; 3-D PBC
>
> ; nblist cut-off
> ; NBOND CUTNB  (see notes on ELEC below)
> ;rlist               = 1.4 ; Cut-off for making neighbor list (short range
> forces). This is ignored in GPU
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> ; From the CHARMM docs (ewald.doc):
> ; NBOND EWALD PMEWald KAPPa 0.34 ORDEr 6 CTOFNB 12.0 CUTNB 14.0
> coulombtype         = PME-switch ; Treatment of long range electrostatic
> interactions
> rcoulomb             = 1.2 ; long range electrostatic cut-off
>
> ; Relative dielectric constant for the medium and the reaction field
> epsilon_r           = 1
> epsilon_rf           = 1
>
> ; Method for doing Van der Waals
> ; NBOND VATOM VSWI CTONNB 10.0 CTOFNB 12.0 CUTNB 14.0
> cutoff-scheme     = Verlet
> vdw-type                = Cut-off
> vdw-modifier = Potential-switch
>
> ; cut-off lengths
> rvdw-switch         = 1.0
> rvdw                 = 1.2
>
> ; Apply long range dispersion corrections for Energy and Pressure
> ; NBOND LRC
> DispCorr             = EnerPres ; account for cut-off vdW scheme
>
> ; Seperate tables between energy group pairs
> energygrp_table         =
>
> ; Spacing for the PME/PPPM FFT grid
> ; CHARMM: EWALD recommended spacing: 0.8 A - 1.2 A and 6th Order spline
> fourierspacing       = 0.12
>
> ; EWALD/PME/PPPM parameters
> ; (possibly increase pme_order to 6 to match the CHARMM recommendation)
> pme_order           = 4
> ewald_rtol           = 1e-05
> ewald_geometry       = 3d
> epsilon_surface     = 0
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl               = V-rescale ; modified Berendsen thermostat
> tau_t               = 0.1 0.1 ; time constant, in ps
> tc-grps             = Protein non-Protein ; two coupling groups - more
> accurate
> ref_t               = 300 300 ; reference temperature, one for each group,
> in K
>
> ; Pressure coupling
> Pcoupl               = Parrinello-Rahman ; Pressure coupling on in NPT
> Pcoupltype           = isotropic ; uniform scaling of box vectors
>
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p               = 2.5 ; time constant, in ps
> compressibility     = 4.5e-5 ; isothermal compressibility of water, bar^-1
> ref_p               = 1.0 ; reference pressure, in bar
>
> ; OPTIONS FOR BONDS
> ; CHARMM uses SHAKE with tol 1e-6
> constraints   = h-bonds   ; Constrain hydrogen bonds
> constraint_algorithm = LINCS     ; Type of constraint algorithm
> continuation   = yes       ; Do not constrain the start configuration
> (yes/no)
> lincs_iter = 1 ; accuracy of LINCS
> shake_tol             = 0.0001   ; Relative tolerance of shake
> lincs_order         = 4         ; Highest order in the expansion of the
> constraint coupling matrix
> lincs_warnangle       = 30       ; Rotate over more degrees than
>
> ; Velocity generation
> ;
> gen_vel = no ; Velocity generation is off
>
> ; the output
> ;
> nstxout       = 2500             ; Frequency to write coordinates to output
> trajectory file, save coordinates every 5 ps
> nstvout       = 2500             ; Frequency to write velocities to output
> trajectory file, save velocities every 5 ps
>
> ; Output frequency for energies to log file and energy file
> nstlog       = 2500             ; Frequency to write energies to log file,
> update log file every 5 ps
> nstenergy   = 2500             ; Frequency to write energies to energy
> file, save energies every 5 ps
>
> ; Output frequency and precision for xtc file
> nstxout-compressed     = 2500               ; Frequency to write
> coordinates to xtc trajectory, xtc compressed trajectory every 5 ps
> compressed-x-grps     = System           ; Group(s) to write to xtc
> trajectory
> energygrps   = System ; Group(s) to write to energy file
>
> comm_mode               = Linear              ; remove center of mass
> translation
> nstcomm                 = 1000                ; [steps] frequency of mass
> motion removal
> comm_grps               = System    ; group(s) for center of mass motion
> removal
>

http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

Settings there apply, as well.  Note that there is no such thing as a CHARMM27 
protein force field.  What you are using is CHARMM22/CMAP.  Due to unfortunate 
file naming, the misnomer gets perpetuated.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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