[gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field
Justin Lemkul
jalemkul at vt.edu
Tue Dec 1 13:44:36 CET 2015
On 11/30/15 3:17 PM, Rakesh Ramachandran wrote:
> 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
I wouldn't limit the applicability of CHARMM36 to simply membrane proteins. It
contains updated CMAP parameters that are superior to the old C22/CMAP force
field and thus C36 is recommended in general over C22/CMAP.
> 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.
>
The settings I linked have been thoroughly tested and validated. I do not know
the accuracy of any other settings.
> I also noticed that the Dispcorr is set to 'no', is this ok. Also I
With the CHARMM force field, dispersion correction is only applied in the case
of lipid monolayers, per the link I sent.
> 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.
>
There will be minor differences in ensembles, but average properties should
agree. See, for instance http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00935.
-Justin
> 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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--
==================================================
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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