[gmx-users] genion error!

Qiang Zhong zqiang320 at webmail.hzau.edu.cn
Wed Feb 28 09:23:43 CET 2007

Dear users:
     I want to prepare protein simulation on 0.15mol/l salt concentration,I use
genion command to add ions,After genion,I change cln.top file last line to NA+
61,CL- 41.
   When I execute grompp ,there are warning :

Warning: atom names in cln.top and cln_b4em.gro don't match (CL - Na)
(more than 20 non-matching atom names)
WARNING 1 [file "cln.top", line 9059]:
  102 non-matching atom names
  atom names from cln.top will be used
  atom names from cln_b4em.gro will be ignored

I continue to execute "mdrun nice 0 -v -s cln_em.tpr -o minim_traj.trr -c
minimized.gro -e minim_ener.edr",There are some error:
Fatal error:
Too many LINCS warnings (10190) - aborting to avoid logfile runaway.
This normally happens when your system is not sufficiently equilibrated,or if you
are changing lambda too fast in free energy simulations.
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file, but normally it is better to fix the problem.

 I don't know what happen ,could somebody tell me?
  Thank you very much!

pdb2gmx -f 4cln.pdb -o cln.gro -p cln.top
editconf -f cln.gro -o cln.gro -bt octahedron -c -d 0.75 
genbox -cp cln.gro -cs spc216.gro -o cln_b4ion.gro -p cln.top
grompp -f minim.mdp -c cln_b4ion.gro -p cln.top -o cln_b4ion.tpr
genion -s cln_b4ion.tpr -o cln_b4em.gro -conc 0.15 -neutral
grompp -f minim.mdp -c cln_b4em.gro -p cln.top -o cln_em.tpr
mdrun -nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e
grompp -f fullmd_sol.mdp -c minimized.gro -p cln.top -o fullmd.tpr
mdrun -nice 0 -v -s fullmd.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e

Qiang Zhong
Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education  
College of Animal Sciences and Technology 
Huazhong Agricultural University
Wuhan,Hubei, 430070
PR China

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