[gmx-users] Error in MD
joshidc_in1 at rediffmail.com
Wed Dec 14 09:30:18 CET 2005
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
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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