[gmx-users] Error in MD

Dhananjay joshi joshidc_in1 at rediffmail.com
Wed Dec 14 09:30:18 CET 2005

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.
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