[gmx-users] Flat-bottomed position restraint set
Oliver Stueker
ostueker at gmail.com
Mon Nov 17 14:28:03 CET 2014
>
>
> Dose it means that the position restraints are applied to all the oxyen
> atoms of the water molecules ?
Yes, that should work.
Have a look at http://manual.gromacs.org/programs/gmx-grompp.html (third
paragraph of the description and the -pp flag) and the chapters 5.7.1 and
5.7.3 in the gromacs manual.
Or simply run a short simulation with a few water molecules and a small
sphere-radius. Then you would have had your answer in ~10 minutes instead
of waiting 12 hours. ;-)
Best,
Oliver
On Sun, Nov 16, 2014 at 10:21 PM, liuyong_1007 at dicp.ac.cn <
liuyong_1007 at dicp.ac.cn> wrote:
> Dear Oliver,
>
> From you explaination, I modify the equil.mdp file as
> define = -DPOSRES_WATER
>
> and the topol.top file as :
>
> ; Include forcefield parameters
> #include "amber94.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> Ion 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> ; residue 1 NA rtp NA q +1.0
> 1 Na 1 NA NA 1 1 22.99 ;
> qtot 1
>
> ; Include topology for ions
> #include "amber94.ff/ions.itp"
>
> #ifdef POSRES_ion
> [ position_restraints ]
> ; i funct g r(nm) k
> ; 1 2 1 3.0 30.0
> #endif
>
>
> ; Include water topology
> #include "amber94.ff/spce.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct g r(nm) k
> 1 2 1 3.0 30.0
> ; 2 2 1 3.0 30.0
> ; 3 2 1 3.0 30.0
> #endif
>
>
> Dose it means that the position restraints are applied to all the oxyen
> atoms of the water molecules ?
>
> Best regards,
> Yong Liu
>
>
>
> liuyong_1007 at dicp.ac.cn
>
> From: Oliver Stueker
> Date: 2014-11-17 00:46
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Flat-bottomed position restraint set
> Dear Liuyoung,
>
>
> in your equil.mdp
> you have
> :
>
> > define = -D
> >
> > *POSRES*
>
>
>
> and in your topol.top:
>
>
>
> > #ifdef
> > *POSRES_WATER*
> > ; Position restraint for each water oxygen
> > ;[ position_restraints ]
> > ; i funct fcx fcy fcz
> > ; 1 1 1000 1000 1000
> > [ position_restraints ]
> > ; i funct g r(nm) k
> > 1 2 1 3.0 30.0
> > ; 2 2 1 3.0 30.0
> > ; 3 2 1 3.0 30.0
> > #endif
>
>
> That means your position_restraints directive will not be included.
>
> Use whatever word you like for both the define and ifdef line, as long as
> it's the same.
> e.g. define -DPOSRES and #ifdef POSRES
> or define -DPOSRES_FLATBOTTOM and #ifdef POSRES_FLATBOTTOM
>
>
> Best,
> Oliver
>
>
>
> On Sat, Nov 15, 2014 at 11:11 PM, liuyong_1007 at dicp.ac.cn <
> liuyong_1007 at dicp.ac.cn> wrote:
>
> > The content of the equil.mdp and topol.top files is shown as follow.
> >
> >
> > equil.mdp:
> >
> > title = NVT Equilibration for Na in 56 water
> > ; Run parameters
> > integrator = md ; leap-frog integrator
> > nsteps = 250000000 ; 2 * 50,000 = 100 ps ;(100 ns)
> > dt = 0.002 ; 2 fs
> >
> > define = -DPOSRES
> > ; Output control
> > nstxout = 500 ; save coordinates every 0.1 ps
> > nstvout = 500 ; save velocities every 1 ps
> > nstenergy = 500 ; save energies every 1 ps
> > nstlog = 500 ; update log file every 1 ps
> > nstxtcout = 500
> > xtc-precision = 1000
> > ; Bond parameters
> > continuation = yes ; Restarting after NVT
> > constraint_algorithm = ; holonomic constraints
> > constraints =h-angles ;water both bond and angle constrained
> > ;constraints = hbonds ; all bonds (even heavy atom-H bonds)
> > constrained
> > lincs_iter = 1 ; accuracy of LINCS
> > lincs_order = 4 ; also related to accuracy
> > ; Neighborsearching
> > ns_type = grid ; search neighboring grid cels
> > nstlist = 1 ; 10 fs
> > rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> > ; vdw
> > vdw-type = Cut-off
> > rvdw = 3.0 ; short-range van der Waals cutoff (in nm)
> > ; Electrostatics
> > coulombtype = cut-off ;Reaction-Field ;Generalized-Reaction-Field
> ;cut-off
> > rcoulomb = 3.0 ; short-range electrostatic cutoff (in nm)
> > epsilon_rf = 2.0
> > epsilon_r = 0.5
> > cutoff-scheme = group
> > ;pme_order = 4 ; cubic interpolation
> > ;fourierspacing = 0.16 ; grid spacing for FFT
> > ; Temperature coupling is on
> > ; annealing = single
> > ; annealing_time = 0 400 1600 2400 4000 5600 7200 10400
> > 13600 16800 ; 230 260 270 300 330 360
> > ; annealing_temp =0 20 40 60 80 100 120 140
> > 160 180 ; 200 220 240 260 280 300
> > ; annealing_npoints = 10
> > ; Temperature coupling is on
> > tcoupl = nose-hoover ;v-rescale; berendsen; nose-hoover ; More
> > accurate thermostat
> > tc-grps = system ; three coupling groups - more accurate
> > tau_t = 0.1 ; time constant, in ps
> > ref_t = 547 ; reference temperature, one for each group, in K
> > ; Pressure coupling is on
> > pcoupl = no ; Pressure coupling on in NPT
> > pcoupltype = semiisotropic ; uniform scaling of x-y box vectors,
> > independent z
> > tau_p = 5.0 ; 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 = no ; 3-D PBC
> > ; Velocity generation
> > gen_vel = no ; assign velocities from Maxwell distribution
> > gen_temp = 133 ; temperature for Maxwell distribution
> > gen_seed = -1 ; generate a random seed
> > ; COM motion removal
> > ; These options remove motion of the protein/bilayer relative to the
> > solvent/ions
> > nstcomm = 1
> > comm-mode = Linear ;ANGULAR;Linear
> > comm-grps =
> >
> >
> >
> >
> >
> >
> >
> > ################################################################
> > topol.top :
> >
> > ;
> > ; File '250_NA_cen.top' was generated
> > ; By user: onbekend (0)
> > ; On host: onbekend
> > ; At date: Tue Aug 12 09:46:55 2014
> > ;
> > ; This is a standalone topology file
> > ;
> > ; It was generated using program:
> > ; pdb2gmx_d - VERSION 4.5.5
> > ;
> > ; Command line was:
> > ; pdb2gmx_d -f water250_NA_cen.pdb -p 250_NA_cen.top -o 250_NA_cen.gro
> > ;
> > ; Force field was read from the standard Gromacs share directory.
> > ;
> >
> > ; Include forcefield parameters
> > #include "amber94.ff/forcefield.itp"
> >
> > [ moleculetype ]
> > ; Name nrexcl
> > Ion 3
> >
> > [ atoms ]
> > ; nr type resnr residue atom cgnr charge mass
> > typeB chargeB massB
> > ; residue 1 NA rtp NA q +1.0
> > 1 Na 1 NA NA 1 1 22.99 ;
> > qtot 1
> >
> > ; Include Position restraint file
> > #ifdef POSRES
> > ;#include "posre.itp"
> > ;[ position_restraints ]
> > ; i funct g r(nm) k
> > ; 1 2 1 3.0 30.0
> > #endif
> >
> >
> > ; Include water topology
> > #include "amber94.ff/spce.itp"
> >
> > #ifdef POSRES_WATER
> > ; Position restraint for each water oxygen
> > ;[ position_restraints ]
> > ; i funct fcx fcy fcz
> > ; 1 1 1000 1000 1000
> > [ position_restraints ]
> > ; i funct g r(nm) k
> > 1 2 1 3.0 30.0
> > ; 2 2 1 3.0 30.0
> > ; 3 2 1 3.0 30.0
> > #endif
> >
> > ; Include topology for ions
> > #include "amber94.ff/ions.itp"
> >
> > [ system ]
> > ; Name
> > Protein
> >
> > [ molecules ]
> > ; Compound #mols
> > Ion 1
> > SOL 250
> >
> >
> >
> >
> >
> > liuyong_1007 at dicp.ac.cn
> >
> > From: liuyong_1007 at dicp.ac.cn
> > Date: 2014-11-16 10:32
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] Flat-bottomed position restraint set
> > Dear Erik,
> >
> > Thanks for your reply! I use a larger cut-off of the non-bonded
> > interaction. But water molecules sitll escape to the vacuum after a 220
> ns
> > MD run.
> > The restraints are applied to the O atoms. Could you please help me to
> > check whether the sets of the equil.mdp and topol.top files are right or
> > wrong?
> > The files are shown in the attachment. Thank you very much !
> >
> > Best regards,
> > Yong Liu
> >
> > liuyong_1007 at dicp.ac.cn
> >
> > From: Erik Marklund
> > Date: 2014-11-14 19:24
> > To: <gmx-users at gromacs.org>
> > Subject: Re: [gmx-users] Flat-bottomed position restraint set
> > Dear Liuyoung,
> >
> > Remember that the electrostatic screening is much weaker in gas phase
> > systems such as yours. I would use a larger cut-off for the non-bonded
> > interactions to effectively have all vs all interactions. Your system is
> > fairly small so you won't be simulating for that long anyway. Note that
> > gromacs can be told to keep the neighbour list from the first frame,
> which
> > would speed up things a bit.
> >
> > Kind regards,
> > Erik
> >
> >
> > Erik Marklund, PhD
> > Postdoctoral Research Fellow, Fulford JRF
> >
> > Department of Chemistry
> > Physical & Theoretical Chemistry Laboratory
> > University of Oxford
> > South Parks Road
> > Oxford
> > OX1 3QZ
> >
> > On 14 Nov 2014, at 07:15, liuyong_1007 at dicp.ac.cn<mailto:
> > liuyong_1007 at dicp.ac.cn> wrote:
> >
> > Hi Justin!
> > I try to apply restraint just to the O atom. There is another question
> > about the set of the coulomb and the vdw interaction for the ion-water
> > cluster Na(H2O)_250. My set is shown as follow:
> >
> > ; vdw
> > vdw-type = Cut-off
> > rvdw = 1.0 ; short-range van der Waals cutoff (in
> nm)
> > ; Electrostatics
> > coulombtype = cut-off ;Reaction-Field ;Generalized-Reaction-Field
> > ;cut-off ^M
> > rcoulomb = 1.2 ; short-range electrostatic cutoff (in
> > nm)^M
> > epsilon_rf = 2.0
> > epsilon_r = 0.5
> > cutoff-scheme = group
> >
> > The radius of the cluster is about 1.12 nm. Is this set appropriate ?
> >
> > Best regards,
> > Yong Liu
> >
> >
> >
> > liuyong_1007 at dicp.ac.cn<mailto:liuyong_1007 at dicp.ac.cn>
> >
> > From: Justin Lemkul
> > Date: 2014-11-14 10:40
> > To: gmx-users
> > Subject: Re: [gmx-users] Flat-bottomed position restraint set
> >
> >
> > On 11/13/14 7:15 PM, liuyong_1007 at dicp.ac.cn wrote:
> > Hi Justin!
> > I use the geometric center of the sphere as the reference coordinates.
> > However, there are still water molecules escaping to the vacuum. Is there
> > other way to aovid this ?
> >
> >
> > This shouldn't happen if things are set up right. Try applying the
> > restraint
> > just to the O atom, not all 3 atoms of the water individually. We do
> this
> > routinely and it works quite well.
> >
> > -Justin
> >
> > Best regards,
> > Yong Liu
> >
> >
> >
> > liuyong_1007 at dicp.ac.cn
> >
> > From: Justin Lemkul
> > Date: 2014-11-12 21:54
> > To: gmx-users
> > Subject: Re: [gmx-users] Flat-bottomed position restraint set
> >
> >
> > On 11/12/14 8:08 AM, liuyong_1007 at dicp.ac.cn wrote:
> > Dear Gromacs users!
> >
> > I use the flat-bottomed position restraints to avoid the molecules to
> > escape from the clusters to the vacuum. The parameters of the restraints
> on
> > water molecules are shown as follow:
> > #ifdef POSRES_WATER
> > ; Position restraint for each water oxygen
> > [ position_restraints ]
> > ; i funct g r(nm) k
> > 1 2 1 3 30.0
> > 2 2 1 3 30.0
> > 3 2 1 3 30.0
> > #endif
> > However, water molecules still escape away from the cluster to the vacuum
> > after about 100 ns MD run at 550K. What should be done with the
> restraints
> > to avoid the water molecules to escape to the vacuum?
> >
> >
> > Are you using suitable reference coordinates passed to grompp -r? If
> > you're
> > not, then the reference coordinates are whatever is in grompp -c, which
> > means
> > your water molecules can deviate up to 3 nm from that position without
> > penalty.
> > For a sphere, the reference coordinates for the water should be the
> > geometric
> > center of the sphere.
> >
> > -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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