You neglected to mention what Force Field you are using. See Also: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060752.html
On 2012-07-03 10:47:25AM -0400, zifeng li wrote: > Dear users, > > I use gromacs version 4.5.4 and is building residues of my own polymer which > has a ester group (COOR). Should I consider the ester as one neutral > group or split it into two groups( -COO and -R) ? > > Here's some information I find: > > 1. Should consider them as one group. Based on the fact that Gromacs > consider a charge group to be a particle so that if I make a > non-neutral charge group, the total charge within a verlet list might > not be 0 if > these two groups are not included in a list at the same time. > > 2. Should split into two groups. First, on Gromacs website, it is said > the charge group usually includes 4 or less atoms. Second, > in aminoacids.rtp file, I find some aminoacids, like Asn, which do > have a non-neutral charge group. > > Would this make a difference? > > Thanks in advance, > > -Zifeng > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists