[gmx-users] Flat-bottomed position restraint set
liuyong_1007 at dicp.ac.cn
liuyong_1007 at dicp.ac.cn
Sun Nov 16 03:42:07 CET 2014
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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