Well, when I look into my .top file, almost no where I see closeness to an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91 sometimes. But I can not see a clear trend on where things go wrong. My protein has only 37 amino acids with 451 atoms (including hydrogens). I am not sure if I can attach the .top file to my e-mail for you to check. This way I could learn where and how things go wrong!
Payman On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote: > > Paymon Pirzadeh wrote: > > 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 > > No, it's not. It's NA+. From ions.itp in the #ifdef _FF_OPLS section: > > [ moleculetype ] > ; molname nrexcl > NA+ 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge mass > 1 opls_407 1 NA+ NA 1 1 > 22.98977 > > > -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! > > > > I am somewhat troubled by the magnitude of charge discrepancy. Look in the > .top > to see where things start going wrong (i.e., not an integer). I would think > your system would have to be quite large to accumulate such a difference in > charge. > > -Justin > > > 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 > > > _______________________________________________ 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