[gmx-users] non-symmetric matrix and too large first values

[medeawan at sohu.com]

Thanks for your answer David:

Maybe I should give more detail about my calculation. The protein structures are getting from PDB and the DNA structures are building by insightII. In order to do the EM, I add the DNA H database to ffG43b1.hdb, and edit the ffG43b1.rtp to let the nucleic acids join together.

I can give the commands I use step by step:

pdb2gmx -f 1iii.pdb -p 2iii.top -o 2iii.gro -i 2iii.itp -ignh
grompp_d -f em -c 2iii -p 2iii -o in -po in
mdrun_d -v -s in -o af -c af -e af -g af -nice 0
grompp_d -v -t af.trr -f nm.mdp -c af.gro -p 2iii.top -o bn.tpr -po bn.mdp
mdrun_d -v -s bn.tpr -g h.log -mtx h.mtx
g_nmeig_d -f h.mtx -s bn.tpr -o v.xvg -v v.trr

And the input file em.mdp:
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  cg
nsteps              =  50000
;
;	Energy minimizing stuff
;
emtol               =  0.000000001
emstep              =  0.000001
nstcgsteep          =  1000

pbc                 =  no 
nstlist             =  0 
nstcomm             =  1
ns_type             =  simple
rlist               =  0
rcoulomb            =  0
rvdw                =  0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no

the input nm.mdp:
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  nm
nsteps              =  100000
;
pbc                 =  no
nstcomm             =  1
ns_type             =  simple
rlist               =  0
rcoulomb            =  0
rvdw                =  0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no

Thanks for any help.
                                          Sincerely yours
                                          Medeawan