[gmx-users] G53A6, non-symmetric selection metrix

[Mohsen Ramezanpour]

Thanks Tom!

Got it! now I know how to interpret this table. Great

Cheers
Mohsen



On Fri, Dec 11, 2015 at 4:12 AM, Piggot T. <T.Piggot at soton.ac.uk> wrote:

> Hi Mohsen,
>
> This table can indeed be quite confusing at first. I suggest you take a
> look at http://redmine.gromacs.org/issues/773#note-10 where there is a
> discussion of how to interpret table 8 (for a specific example, but it
> should highlight how it works). Hopefully that should answer your questions.
>
> Cheers
>
> Tom
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mohsen
> Ramezanpour [ramezanpour.mohsen at gmail.com]
> Sent: 10 December 2015 23:42
> To: Discussion list for GROMACS users
> Subject: [gmx-users] G53A6, non-symmetric selection metrix
>
> Dear All,
>
> Reading the parameters for Gromos 53A6 ff ( article by Oostenbrink  *et al.
> Journal of computational chemistry* 25.13 (2004): 1656-1676.), I got
> confused about van der waals interactions between non-bonded atoms.
>
> for two atom types, we use combination rules to get (Cij 6) and (Cij 12),
> and these combination rules (eq. 15 in article) make use of selection
> matrix (table 8 in article). However this selection matrix is not
> symmetric.
>
> This means L-J interactions between two atom types depends to the order we
> put them in [pairs]. Is it correct?
>
> If this is true, then the order of atom numbers in [pair] matters. But it
> does not make sense, why (Cij 12) should be different from (Cji 12)?
>
> Thanks in advance for your comments
>
> Best,
> Mohsen
>
> --
> *Rewards work better than punishment ...*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
*Rewards work better than punishment ...*