[gmx-users] genion error!

Triguero, Luciano O ltriguero at miami.edu
Wed Feb 28 15:26:48 CET 2007

Hi Zhong,

It seems that you are not using the correct <fn>.top file. Once you finish adding ions with genion, you will need to generate 
a new topology, which also contains ions.



Dr. Luciano Triguero
College of Art and Science
Department of Chemistry
Cox Science Building
1301 Memorial Drive, Room 146
P.O Box 249118
Coral Gables, FL 33124-0431
Cellular: 305-904-2419
Office: 305-284-3938

-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Qiang Zhong
Sent: Wed 2/28/2007 3:23 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] genion error!
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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