[gmx-users] Re: problem while running grompp Pocition restrined dynamics
Yang Ye
leafyoung81-group at yahoo.com
Wed Apr 12 12:44:21 CEST 2006
It is not how to increase it but how to avoid it.
Try to have longer equilibration time before production MD.
Yang Ye
santosh naik wrote:
> 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
>>>> _______________________________________________
>>>> 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
>>>
>>>
> _______________________________________________
> 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
>
>
More information about the gromacs.org_gmx-users
mailing list