[gmx-users] How to assign charge group for ester?
Peter C. Lai
pcl at uab.edu
Tue Jul 3 22:45:25 CEST 2012
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,
> gmx-users mailing list gmx-users at gromacs.org
> * 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-request at 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
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
More information about the gromacs.org_gmx-users