[gmx-users] gromacs.org_gmx-users Digest, Vol 133, Issue 30
Eudes Fileti
fileti at gmail.com
Wed May 6 19:13:24 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>
wrote:
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> Today's Topics:
>
> 1. Re: Constraint of active site in gromacs (Mark Abraham)
> 2. Re: Constraint of active site in gromacs (Nataraj Balakrishnan)
> 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)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 06 May 2015 14:37:38 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Constraint of active site in gromacs
> Message-ID:
> <
> CAMNuMARHm6ieYiJUTEGdoSf2Ok7qekKcxBKTfom43YNj02RmvA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Yes, but you need distance restraints (not constraints, which are
> different) like Justin said. You also need to get both ligating water
> molecules, protein and ion into the same moleculetype to make that work.
> That's not trivial, so make sure you really need that EM for something.
>
> Mark
>
> On Wed, 6 May 2015 15:57 Raj D <gromacs.for.f at gmail.com> wrote:
>
> > Thanks Justin , but I have a modelled protein download from Modbase and
> > added Fe iron into the approximate ligating distance of three ligating
> > atoms of the amino acids. Now I am aiming to bring the octahedral
> geometry
> > of the Fe coordinating atoms which include two more water molecules using
> > EM engine of Gromacs. Will it be possible to let the EM to optimize the
> > distances between the atoms of the octahedral by constraining the angles
> > and positions of the atom positions for a octahedral geometry ?
> > Regards,
> > Raja
> > On May 6, 2015 5:14 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 5/6/15 3:09 AM, Raj D wrote:
> > >
> > >> Dear User,
> > >> I would like to constraint the Iron bound active site of the protein
> in
> > >> octahedral shape in EM and MD steps ... Is there a direct routine to
> > >> create
> > >> such a constraint in gromacs by feeding information of ligating atoms
> of
> > >> amino acids with Iron at the center of the octahedral geometry.
> > >>
> > >
> > > What you need are distance restraints, which you will have to write in
> > the
> > > topology yourself.
> > >
> > > -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
> > >
> > > ==================================================
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
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> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> >
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 6 May 2015 20:23:06 +0530
> From: Nataraj Balakrishnan <natarajmtech at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Constraint of active site in gromacs
> Message-ID:
> <CALWW=Y+X_MOacvV3sua+0-CvBDiYKoKv2OZeGbEDF3Rj=
> HKCLQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Thanks Mark, I will do that .
> Regards,
> Raja
> On May 6, 2015 8:07 PM, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>
> > Yes, but you need distance restraints (not constraints, which are
> > different) like Justin said. You also need to get both ligating water
> > molecules, protein and ion into the same moleculetype to make that work.
> > That's not trivial, so make sure you really need that EM for something.
> >
> > Mark
> >
> > On Wed, 6 May 2015 15:57 Raj D <gromacs.for.f at gmail.com> wrote:
> >
> > > Thanks Justin , but I have a modelled protein download from Modbase and
> > > added Fe iron into the approximate ligating distance of three ligating
> > > atoms of the amino acids. Now I am aiming to bring the octahedral
> > geometry
> > > of the Fe coordinating atoms which include two more water molecules
> using
> > > EM engine of Gromacs. Will it be possible to let the EM to optimize the
> > > distances between the atoms of the octahedral by constraining the
> angles
> > > and positions of the atom positions for a octahedral geometry ?
> > > Regards,
> > > Raja
> > > On May 6, 2015 5:14 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
> > >
> > > >
> > > >
> > > > On 5/6/15 3:09 AM, Raj D wrote:
> > > >
> > > >> Dear User,
> > > >> I would like to constraint the Iron bound active site of the protein
> > in
> > > >> octahedral shape in EM and MD steps ... Is there a direct routine to
> > > >> create
> > > >> such a constraint in gromacs by feeding information of ligating
> atoms
> > of
> > > >> amino acids with Iron at the center of the octahedral geometry.
> > > >>
> > > >
> > > > What you need are distance restraints, which you will have to write
> in
> > > the
> > > > topology yourself.
> > > >
> > > > -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
> > > >
> > > > ==================================================
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
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> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 6 May 2015 23:00:43 +0800 (CST)
> From: Brett <brettliu123 at 163.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] on a MD run notice
> Message-ID: <1cecbc8.27072.14d29be3e22.Coremail.brettliu123 at 163.com>
> Content-Type: text/plain; charset=GBK
>
> Dear All,
>
> For a NVT equilibration MD, I got the following notice. Will you please
> advice me whether the notice just told me I have wasted my computation
> resource, or I need to redo my NVT equilibration.
>
> I am looking forward to getting your reply.
>
> Brett
>
>
> verage load imbalance: 7.7 %
> Part of the total run time spent waiting due to load imbalance: 3.8 %
> Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X
> 0 % Y 0 %
> Average PME mesh/force load: 0.228
> Part of the total run time spent waiting due to PP/PME imbalance: 9.3 %
>
> NOTE: 9.3 % performance was lost because the PME ranks
> had less work to do than the PP ranks.
> You might want to decrease the number of PME ranks
> or decrease the cut-off and the grid spacing.
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 06 May 2015 11:18:28 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] on a MD run notice
> Message-ID: <554A30C4.1050606 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/6/15 11:00 AM, Brett wrote:
> > Dear All,
> >
> > For a NVT equilibration MD, I got the following notice. Will you please
> advice me whether the notice just told me I have wasted my computation
> resource, or I need to redo my NVT equilibration.
> >
>
> It's just performance loss; there's nothing wrong (from this message) with
> the
> simulation.
>
> -Justin
>
> > I am looking forward to getting your reply.
> >
> > Brett
> >
> >
> > verage load imbalance: 7.7 %
> > Part of the total run time spent waiting due to load imbalance: 3.8 %
> > Steps where the load balancing was limited by -rdd, -rcon and/or -dds:
> X 0 % Y 0 %
> > Average PME mesh/force load: 0.228
> > Part of the total run time spent waiting due to PP/PME imbalance: 9.3 %
> >
> > NOTE: 9.3 % performance was lost because the PME ranks
> > had less work to do than the PP ranks.
> > You might want to decrease the number of PME ranks
> > or decrease the cut-off and the grid spacing.
> >
> >
> >
>
> --
> ==================================================
>
> 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
>
> ==================================================
>
>
> ------------------------------
>
> 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
>
> ==================================================
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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