[gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field
Rakesh Ramachandran
korenpol3 at gmail.com
Mon Nov 30 21:17:47 CET 2015
Hi Justin,
Thanks for the reply. I have few more doubts. I had mentioned CHARMM27
just for consistency with Gromacs naming. In the website it mentions that
those settings are for CHARMM36 and I read at lot of places that this force
field is good mainly for membrane proteins, so is it ok for me to use it
with CHARMM22/CMAP. Moreover I am using Verlet cutoff with GPU, so are
these options still applicable or I have to use vdw-modifier:
potential-shift-verlet.
I also noticed that the Dispcorr is set to 'no', is this ok. Also I
prepared my input files with CHARMM-GUI and I see tau_t - 1.0 and tau_p 5.0
whereas your tutorial has different values. I am confused as to how to
determine the optimal set of parameters and are all these parameters
optimal for CHARMM36 only.
I would be grateful if you could let me know what kind of tests or values
one needs to check to know if the parameters are appropriate for running md
with a protein in a particular force field or point me to the relevant
literature.
On 30 November 2015 at 06:10, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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