Dear Gromacs users, I use gromacs version 4.5.4 and build residue of my own polymers which has a ester group (COOR). From aminoacids.atp database, I found the partial charge of each atom, where the carbolic group COO- is not neutron and has to be neutralized by a methyl group. Should I consider the ester as one neutral group or split it into two groups?
Here's some exploration I have done: 1. Should consider them as one group. Based on the fact that Gromacs consider a charge group to be a moving particle so that if I make a non-neutral charge group ( i.e., COO- , methyl connected to it as two charge groups), the total charge of 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. Considering this, it seems that I have to split the ester group into two groups. Second, in aminoacids.rtp file, I find some aminoacids, like Asn, which do have a non-neutral charge group. Would this really make a difference? Thanks in advance, -Zifeng -- 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/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