[gmx-users] Hydroxide Ion
tsjerkw at gmail.com
Thu Jul 16 19:37:54 CEST 2009
Well, it's not just a matter of topology. This is only true if the
basic assumption holds, that the particles behave approximately
classical. This is definitely not the case for species such as
hydroxide and hydronium.
On Thu, Jul 16, 2009 at 4:13 AM, Justin A. Lemkul<jalemkul at vt.edu> wrote:
> Marc Charendoff wrote:
>> I am needing to include a single hydroxide ion in my simulation - is
>> there a force field available in Gromacs that is already parameterized, or
>> do I need to create from scratch? With regards to topology, same question,
>> especially as PRODRG does not do mono or diatomics. Any guidance anyone
>> could provide would be very much appreciated. I have tried searching the
>> archives but didn't find anything.
> No, you'll need to do it yourself. The topology should be trivial - two
> atoms, one bond. As for what parameters to assign, there you've got your
> work cut out for you.
>> Marc Charendoff
>> 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
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> 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