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_1...@dicp.ac.cn < liuyong_1...@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_1...@dicp.ac.cn > > From: liuyong_1...@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_1...@dicp.ac.cn > > From: Erik Marklund > Date: 2014-11-14 19:24 > To: <gmx-us...@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_1...@dicp.ac.cn<mailto: > liuyong_1...@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_1...@dicp.ac.cn<mailto:liuyong_1...@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_1...@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_1...@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_1...@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 > > jalem...@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-requ...@gromacs.org.