[gmx-users] metal ion go out of protein after md
tsjerkw at gmail.com
Wed Mar 11 10:26:04 CET 2009
Nothing, except reading more about periodic boundary conditions. It
doesn't hurt though to understand that binding of ions such as Mn to
proteins involves charge transfer effects, that are hard to model
properly. This will cause a (further) deviation between your results
and reality. So be careful in drawing conclusions.
On Wed, Mar 11, 2009 at 8:41 AM, Homa Azizian <hazizian at razi.tums.ac.ir> wrote:
> MN in my active site participate in electrostatic intraction. I did not
> define any covalant bonds in topology file.
> What should I do in the case of Electrostatic intraction?
> Tehran University of Medical Sciences
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
> gmx-users mailing list gmx-users at gromacs.org
> 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
More information about the gromacs.org_gmx-users