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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ***************************************************************** Pär Bjelkmar Stockholm Center for Biomembrane Research Tel: +46-8-16 2746 Dep of Biochemistry and Biophysics Fax: +46-8-15 3679 Stockholm University [EMAIL PROTECTED] 10691 Stockholm, Sweden ***************************************************************** _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
