[[gmx-users] genion error!]

[Pär Bjelkmar]

Maybe you forgot to delete the waters that were removed in the
ionization process?

/Pär

> 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
> minim_ener.edr
> 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
> md_ener.edr
>
>
>
>
> ------------------------------
> 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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-- 
*****************************************************************
Pär Bjelkmar            Stockholm Center for Biomembrane Research
Tel: +46-8-16 2746      Dep of Biochemistry and Biophysics
Fax: +46-8-15 3679      Stockholm University
bjelkmar at cbr.su.se      10691 Stockholm, Sweden
*****************************************************************