[gmx-users] Re: problem while running grompp Pocition restrined dynamics

[santosh naik]

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
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list.
> >Use the
> > www interface or send it to
> >gmx-users-request at gromacs.org.
> > Can't post? Read
> >http://www.gromacs.org/mailing_lists/users.php
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>