[gmx-users] Re: problem while running grompp Pocition restrined dynamics
santosh naik
btsanty at gmail.com
Wed Apr 12 11:28:26 CEST 2006
Warning: 1-4 interaction between 1124 and 1137 at distance 1.973 which
is larger than the 1-4 table size 1.000 nm
i got this warning while running the simulation
how could i increase it
On 4/12/06, santosh naik <btsanty at gmail.com> wrote:
> 7/out7.gro is the out put of mdrun i have run for em
>
>
> On 4/12/06, X.Periole <X.Periole at rug.nl> wrote:
> >
> > Your topology file does not correspond to the coordinate
> > file. You got to check both of them but the error is
> > certainly coming from the topology file. Not that you need
> > to include the ions.itp file after incerting the ions.
> >
> > It is better to insert the ions in the solvent Temp bath
> > and not in a separate bath.
> >
> > Your vdW cutoff is 1.0 nm. This is short if you do not do
> > it for a particular reason.
> >
> > You do not use indexes !! grompp does not complain about
> > non-defined groups ??
> >
> > For the last grompp you run you give the 7/out7.gro as
> > starting configuration (-c option) which does not seem
> > to be the output of your em !!
> >
> > Solvating with genion is a new feature of GROMCAS ??? You
> > meant genbox probably.
> >
> > XAvier
> >
> > > hi guys
> > > i am working with the spider toxin protein and as
> > >mentioned early i
> > > was unable 2 over come this process
> > >
> > > below i have mentioning my problem in detail
> > >
> > > first i take the protein and run the pdb2 gmx command
> > >under the
> > > gromacs force field
> > >
> > > pdb2gmx -f spider.pdb -o 1/out1.gro -p 1/out1.top
> > >
> > > then i run the edit conf
> > >
> > > editconf -bt octahedron -f 1/out1.gro -o 2/out2.gro -c
> > >-d 0.7
> > >
> > > then i solvates the box using genion
> > > genion -cp 2/out2.gro -cs spc216.gro -o 3/out3.gro -p
> > >1/out1.top
> > >
> > > then i run the grompp for energy minimisation
> > > using the em.mdp file given below
> > >
> > > title = drg_trp
> > > cpp = /usr/bin/cpp
> > > define = -DFLEX_SPC
> > > constraints = none
> > > integrator = steep
> > > dt = 0.002 ; ps !
> > > nsteps = 500
> > > nstlist = 10
> > > ns_type = grid
> > > rlist = 0.9
> > > coulombtype = PME ; Use particle-mesh ewald
> > > rcoulomb = 0.9
> > > rvdw = 1.0
> > > fourierspacing = 0.12
> > > fourier_nx = 0
> > > fourier_ny = 0
> > > fourier_nz = 0
> > > pme_order = 4
> > > ewald_rtol = le-5
> > > optimize_fft = yes
> > > ;
> > > ; Energy minimizing stuff
> > > ;
> > > emtol = 1000.0
> > > emstep = 0.01
> > >
> > >
> > > grompp -f em.mdp -c 3/out3.gro -p 1/out1.top -o
> > >4/out4.tpr
> > >
> > > here i got one note
> > > NOTE:
> > > System has non-zero total charge: 2.000000e+00
> > >
> > > then i used the genion command
> > > genion -s 4/out4.tpr -o 5/out5.gro -nname Cl -nn 2 -g
> > >5/out5.log
> > >
> > > now again i run the grompp
> > > now here i have edited the top file
> > > i removed 2 water molecule and added 2 cl molecules
> > > grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o
> > >6/out6.tpr
> > >
> > > then i have run the mdrun
> > > nohup mdrun -s 6/out6.tpr -o 7/out7.trr -c 7/out7.gro -g
> > >7/out7.log -e
> > > 7/out7.edr &
> > >
> > > then i tried to run the position restrained dynamic so i
> > >have tried with grompp
> > >
> > > using mdp file given below
> > > title = trp_drg
> > > warnings = 10
> > > cpp = /lib/cpp ; location of cpp on SGI
> > > define = -DPOSRES
> > > constraints = all-bonds
> > > integrator = md
> > > dt = 0.002 ; ps !
> > > nsteps = 10000 ; total 20.0 ps.
> > > nstcomm = 1
> > > nstxout = 250 ; output coordinates every
> > >0.5 ps
> > > nstvout = 1000 ; output velocities every
> > >2.0 ps
> > > nstfout = 0
> > > nstlog = 10
> > > nstenergy = 10
> > > nstlist = 10
> > > ns_type = grid
> > > rlist = 0.9
> > > coulombtype = PME
> > > rcoulomb = 0.9
> > > rvdw = 1.0
> > > fourierspacing = 0.12
> > > fourier_nx = 0
> > > fourier_ny = 0
> > > fourier_nz = 0
> > > pme_order = 6
> > > ewald_rtol = 1e-5
> > > optimize_fft = yes
> > > ; Berendsen temperature coupling is on in four groups
> > > Tcoupl = berendsen
> > > tau_t = 0.1 0.1 0.1 0.1
> > > tc_grps = protein IN4 sol Cl-
> > > ref_t = 300 300 300 300
> > > ; Pressure coupling is on
> > > Pcoupl = berendsen
> > > pcoupltype = isotropic
> > > tau_p = 0.5
> > > compressibility = 4.5e-5
> > > ref_p = 1.0
> > > ; Generate velocites is on at 300 K.
> > > gen_vel = yes
> > > gen_temp = 300.0
> > > gen_seed = 173529
> > >
> > > grompp -f pr.mdp -c 7/out7.gro -p 1/out1.top -o
> > >8/out8.tpr
> > >
> > > here i got he error
> > >
> > >Fatal error:
> > > number of coordinates in coordinate file (7/out7.gro,
> > >7485)
> > > does not match topology (1/out1.top, 0)
> > >
> > > can any one help me over this issue
> > >
> > > Thanking you
> > > Santosh Naik
> > > _______________________________________________
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