[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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