Something seems wrong with your topology. It seems grompp gets
confused about CL in one file being Na in the other. Maybe you added
the last lines to cln.top in the wrong order. It doesn't necessarily
cause the LINCS error later on, but suggests that your topology may
need some more work.
/Erik
28 feb 2007 kl. 09.23 skrev Qiang Zhong:
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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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
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