[gmx-users] Flat-bottomed position restraint set
liuyong_1007 at dicp.ac.cn
liuyong_1007 at dicp.ac.cn
Mon Nov 17 02:51:32 CET 2014
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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