[gmx-users] Vacuum simulation in GMX 5 (Justin Lemkul)
Eudes Fileti
fileti at gmail.com
Thu May 7 14:04:33 CEST 2015
Hi Justin, this is my mdp options.
thanks
eef
; Run control
define = -DPOSRES
integrator = sd ; Langevin dynamics
tinit = 0
dt = 0.002
nsteps = 5000000 ; 100 ps
nstcomm = 100
; Output control
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 100
nstenergy = 100
nstxout-compressed = 0
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme = verlet
nstlist = 20
ns_type = grid
pbc = xyz
rlist = 1.2
; Electrostatics
coulombtype = cut-off
rcoulomb = 1.2
; van der Waals
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = no
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; EWALD/PME/PPPM parameters
pme_order = 6
ewald_rtol = 1e-06
epsilon_surface = 0
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = v-rescale
nsttcouple = -1
nh-chain-length = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc-grps = system
; Time constant (ps) and reference temperature (K)
tau-t = 0.1
ref-t = 323
; pressure coupling
Pcoupl = no
Pcoupltype = isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 2.0
compressibility = 4.5e-5
ref-p = 1.0
; Scaling of reference coordinates, No, All or COM
refcoord-scaling = com
; Free energy control stuff
free_energy = yes
init_lambda_state = 0
delta_lambda = 0
calc_lambda_neighbors = 1 ; only immediate neighboring windows
vdw_lambdas = 0.00 0.00 0.00 0....... .70 0.75 0.80 0.85 0.90
0.95 1.00
coul_lambdas = 0.00 0.05 0.10 0........1.00 1.00 1.00 1.00 1.00
1.00 1.00 1.00 1.00
; Options for the decoupling
sc-alpha = 0.5
sc-coul = no ; linear interpolation of Coulomb (none
in this case)
sc-power = 1.0
sc-sigma = 0.3
couple-moltype = Pept ; name of moleculet ype to decouple
couple-lambda0 = vdw-q ; only van der Waals interactions
couple-lambda1 = none ; turn off everything, in this case
only vdW
couple-intramol = yes
nstdhdl = 10
; Generate velocities to start
gen_vel = yes
gen_temp = 300
gen_seed = -1
; options for bonds
constraints = h-bonds ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Do not constrain the starting configuration
continuation = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 12
_______________________________________
Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Rua Talim, 330, São José dos Campos - SP
Página: sites.google.com/site/fileti/
On 6 May 2015 at 14:04, <gromacs.org_gmx-users-request at maillist.sys.kth.se>
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> 3. on a MD run notice (Brett)
> 4. Re: on a MD run notice (Justin Lemkul)
> 5. Vacuum simulation in GMX 5 (Eudes Fileti)
> 6. Re: Vacuum simulation in GMX 5 (Justin Lemkul)
>
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> ----------------------------------------------------------------------
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>
> ------------------------------
>
> Message: 5
> Date: Wed, 6 May 2015 13:54:28 -0300
> From: Eudes Fileti <fileti at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Vacuum simulation in GMX 5
> Message-ID:
> <CAHC5Q=
> gBdFnhMxHNzcPditqELXmSFpQig9UF-ck3C+RjScKXgg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hello,
> in the previous gmx versions I could accelerate simulations in vacuum
> making the cutting cut-offs zero and pbc = no.
>
> However, now it is no longer current possible with GMX 5 (since pbc = no is
> not supported with dd, and the particle decomposition mode is not suported
> in GMX 5).
>
> Does anyone have any tips to speed up a calculation in vacuum?
> I'm decoupling a small molecule in vacuum (for an free energy calculation)
> at a rate of 1ns/h, which seems very slow.
>
> eef
> _______________________________________
> Eudes Eterno Fileti
> Instituto de Ci?ncia e Tecnologia da UNIFESP
> Rua Talim, 330, S?o Jos? dos Campos - SP
> P?gina: sites.google.com/site/fileti/
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 06 May 2015 13:03:47 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Vacuum simulation in GMX 5
> Message-ID: <554A4973.9020008 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 5/6/15 12:54 PM, Eudes Fileti wrote:
> > Hello,
> > in the previous gmx versions I could accelerate simulations in vacuum
> > making the cutting cut-offs zero and pbc = no.
> >
> > However, now it is no longer current possible with GMX 5 (since pbc = no
> is
> > not supported with dd, and the particle decomposition mode is not
> suported
> > in GMX 5).
> >
> > Does anyone have any tips to speed up a calculation in vacuum?
> > I'm decoupling a small molecule in vacuum (for an free energy
> calculation)
> > at a rate of 1ns/h, which seems very slow.
> >
>
> That is really slow. We have been doing some of this lately, and for a
> 50-atom
> molecule I get 130 ns/day on one core. Can you post a full .mdp file?
>
> -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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