[gmx-users] Error in MD

[Tsjerk Wassenaar]

Hi Dhananjay,

You have some serious problems with your starting structure. You may want to
try to energy minimize your system before solvation. If that doesn't work,
inspect your structure for overlapping atoms or crossing bonds.

Cheers,

Tsjerk

On 14 Dec 2005 08:30:18 -0000, Dhananjay joshi <joshidc_in1 at rediffmail.com>
wrote:
>
>
> Hello Mark,
>
> I have again started working on CORE_MTB.pdb
>
> The first step that I took was
>
> 1. pdb2gmx -f CORE_MTB.pdb -o CORE_MTB.gro -p CORE_MTB.top
>
>
> It has generated fatal error as follows
>
> Fatal error:
> Atom HD1 in residue HISB 61 not found in rtp entry with 12 atoms
>             while sorting atoms. Maybe different protonation state.
>             Remove this hydrogen or choose a different protonation state.
>             Option -ignh will ignore all hydrogens in the input.
>
> Then I used -ignh option and the steps are as follows..
>
>
> 2. editconf -f CORE_MTB.gro -o CORE_MTB.gro -d 0.8
>
> WARNING: No boxtype specified - distance condition applied in each
> dimension.
> If the molecule rotates the actual distance will be smaller. You might
> want
> to use a cubic box instead, or why not try a dodecahedron today?
>
> 3. genbox -cp CORE_MTB.gro -cs -o CORE_MTB_b4em.gro -p CORE_MTB.top
>
> 4.grompp -f em.mdp -po em_out.mdp -c CORE_MTB_b4em.gro -p CORE_MTB.top -o
> CORE_MTB_em.tpr
>
>
> 5.mdrun -s CORE_MTB_em.tpr -o CORE_MTB_em.trr -c CORE_MTB_b4pr.gro -e
> em.edr -g em.log
>
> After this I got some message with output as follows
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 2000.
> Potential Energy  =  2.1868101e+17
> Maximum force    =            inf on atom 28916
> Norm of force    =            nan
>
> Could you please tell me what is wrong ?
>
> The mdp file used for grompp amd mdrun is as follows..
>
>
>
> ;      User spoel (236)
> ;      Wed Nov  3 17:12:44 1993
> ;      Input file
> ;
> cpp                =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints        =  none
> integrator          =  steep
> nsteps              =  100
> ;
> ;      Energy minimizing stuff
> ;
> emtol              =  2000
> emstep              =  0.01
>
> nstcomm            =  1
> ns_type            =  grid
> rlist              =  1
> rcoulomb            =  1.0
> rvdw                =  1.0
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel            =  no
>
>
>
> On Tue, 13 Dec 2005 Mark Abraham wrote :
> >Dhananjay joshi wrote:
> >>  Yes Mark,
> >>
> >>You are right.
> >>
> >>using "gmx_dump -s CORE_MTB_em.tpr | less" i found large vector of
> velocities (v) after the large vector of positions (x) and that they are all
> non-zero.
> >>
> >>what should I do now ?
> >
> >>>see if there is a large vector of velocities (v) after the large vector
> of positions (x) and that they are all zero. If they aren't, I suspect you
> haven't actually done as you describe above.
> >
> >grompp is the only thing that can be generating velocities. Check you've
> done what you think you've done.
> >
> >Mark
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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