On 30/12/2011 5:30 AM, Olivia Waring wrote:
Hi Mark,
Thanks for your reply! I'm sorry, you're right, as far as I know the
manual doesn't actually mention Buckingham pairs generation... but
when I set gen-pairs to "yes" and run grompp, I get the following error:
"Generating pair parameters is only supported with LJ non-bonded
interactions"
I guess I'm wondering how anyone can use the Buckingham potential at
all, since Gromacs does not appear to support pairs generation for the
Buckingham or the use of explicitly defined Buckingham pair parameters
(when defining [ pairtypes ], you have to give the parameters in LJ
form).
Why do you need pairs with your model?
Mark
Thanks so much again,
Olivia
On Wed, Dec 28, 2011 at 8:28 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 29/12/11, *Olivia Waring *<owar...@princeton.edu
<mailto:owar...@princeton.edu>> wrote:
I apologize for the truncated message; I pressed send too soon.
According to the Gromacs manual, pairs cannot be generated
automatically for the Buckingham potential,
Where does it say this?
but the [ pairtypes ] directive seems to only accept parameters
in LJ form (i.e. c6 and c12, instead of a, b, and c6). I've been
looking into ways to interconvert between the two potential
forms, but haven't found anything... Can anyone who has
successfully generated a topology using the Buckingham potential
shed light on this issue?
You want a 1-4 interaction using Buckingham functional form? If
so, I don't think GROMACS supports it. If you're trying to combine
bits of force fields that use L-J with bits of force fields that
use Buckingham, then that's almost certainly a bad idea.
Mark
Thank you so much,
Olivia
On Wed, Dec 28, 2011 at 11:05 AM, Olivia Waring
<owar...@princeton.edu <mailto:owar...@princeton.edu>> wrote:
Hello Gromacs users,
I'm using a Buckingham potential for the nonbonded
interactions in my system, so I have the following lines in
my forcefield.itp file:
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ
fudgeQQ
2 1 no 1.0
1.0
--
Olivia Waring (???)
Princeton University '12
AB Chemistry
--
Olivia Waring (???)
Princeton University '12
AB Chemistry
--
gmx-users mailing list gmx-users@gromacs.org
<mailto: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
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
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
