[gmx-users] using charmm36 force field with gromacs
Justin Lemkul
jalemkul at vt.edu
Wed Nov 4 00:00:09 CET 2015
On 11/3/15 5:21 PM, Yoav Atsmon-Raz wrote:
> Thank you so much for your detailed and prompt response Justin, it is much appreciated. Is it correct to assume that I should apply these parameters to all of my protocols and not just the prod. md one (including minimization/equilibration)?
>
Everything.
-Justin
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
> Sent: Tuesday, November 03, 2015 3:11 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] using charmm36 force field with gromacs
>
> On 11/3/15 4:32 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?
>>
>
> Several. See below. There used to be a page on the wiki with all this
> information but it somehow got deleted. I'm trying to get it restored.
>
>> 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
>
> Use constraints = h-bonds
>
> You'll get incorrect balance of 1-4 interactions if you constrain all bonds with
> CHARMM.
>
>> 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
>
> The proper nonbonded settings are:
>
> cutoff-scheme = Verlet
> vdwtype = cutoff
> vdw-modifier = force-switch ; same as vfswitch
> rlist = 1.2 ; will be tuned automatically
> rvdw = 1.2
> rvdw-switch = 1.0
> coulombtype = PME
> rcoulomb = 1.2
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> fourierspacing = 0.12
>
> Note that these are essential for getting membrane properties right.
>
>> ; 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
>
> Do not apply dispersion correction for bilayers. Do apply it for monolayers.
>
> -Justin
>
>> ; 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!
>>
>
> --
> ==================================================
>
> 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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