Thanks for the tips! But I still have problem with my added ion. Justin had told me that ion names are force-field specific! Since I am using OPLSaa, I checked the itp file for Na ion name, and it was Na+. I used this name with the -pname switch, but again during the grompp I ran into the following error: Warning: atom name 65870 in AFP_I.top and AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)
WARNING 1 [file AFP_I.top, line 4151]: 1 non-matching atom name atom names from AFP_I.top will be used atom names from AFP_I_solvated_54_62_102_null.gro will be ignored I really do not know what I am doing wrong here! Also regarding past discussions, adding this single ion has lead into the following note: NOTE 1 [file AFP_I.top, line 4151]: System has non-zero total charge: 1.000000e-02 I am not sure if that much charge will cause me troubles or not! Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: > Paymon Pirzadeh wrote: > > Can I change the charge of Na ion added from +1 to +0.99 to cancel the > > negative charge exactly? Does that hurt science or simulation? > > It's probably irrelevant. The representation of "decimal" numbers on > computers can be inexact, such that things like 0.02 added to itself 100 > times does not pass a test for equality with 2. You may be observing > this kind of thing here. Your protein's [atoms] directive has a running > count of the total charge on the molecule - go and read it and see that > each residue has an integral charge. Hopefully you can observe where the > rounding error might be occurring and you can make a judgement about > whether this might be true. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
