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 [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
