From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Thu Feb 13 2014 - 19:48:12 CST
Please reply to the list, not to people's personal e-mail.
I'll need some more details to be of any help. Is this a lipid or a
cofactor or a drug-like molecule? Are you planning to simulate its
interaction with a biomolecule (such as a protein or nucleic acid)? If
yes, what force field are you planning to use for the biomolecule?
Best regards,
Kenno.
On 02/13/2014 07:12 PM, Anna Borlsky wrote:
> Dear Kenno,
>
> My problem is that I generated the topology and the parameter file using
> xplo-2d and the multiplicities are zero on the parameter file what makes
> no sense so I should change it. My problem is that I do not know which
> values of multiplicities give. All dihedrals with multiplicity 2 is
> probably not ok. I have sp2 carbons on my molecule.
> I have also doubts in attribute multiplicities when I have two dihedrals
> that are the same but only differ on the value of the angle (one with 180º
> and the other one with 0º).
>
> Best regards,
> Anna
>
>
>
>
> 2014-02-13 23:53 GMT+00:00 Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu
> <mailto:kvanomme_at_rx.umaryland.edu>>:
>
> Additionally, users should leave the force fields alone unless they're
> really really sure of what they're doing.
>
>
> On 02/13/2014 03:23 PM, Norman Geist wrote:
>
> Additionally, this has nothing to with namd but with forcefield
> definitions.
>
> Norman Geist.
>
>
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu
> <mailto:owner-namd-l_at_ks.uiuc.edu>
> [mailto:owner-namd-l_at_ks.uiuc.__edu
> <mailto:owner-namd-l_at_ks.uiuc.edu>] Im
> Auftrag von Jeffrey Potoff
> Gesendet: Donnerstag, 13. Februar 2014 18:34
> An: Anna Borlsky
> Cc: namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
> Betreff: Re: namd-l: Dihedrals multiplicity!
>
> On 02/13/2014 12:27 PM, Anna Borlsky wrote:
>
> Dear Jeffrey,
>
> Thank you very much for the link, but I did not found in
> it an answer
> to my question.
> What I see is that when I changed the multiplicity of the
> dihedrals
>
> in
>
> namd the molecule twisted. But I do not know which are the
> right
> multiplicities to use and what does they mean in the
> simulation.
>
> Best regards,
> Vanessa
>
> Try this one:
>
> http://www.ks.uiuc.edu/__Training/Tutorials/science/__forcefield-
> <http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield->
> tutorial/forcefield-html/__node6.html
>
> Specifically, you should read the section entitled "A Closer
> Look at
> Dihedral Parameters"
>
> --
> ==============================__==============================__==========
> Jeffrey J. Potoff jpotoff_at_wayne.edu <mailto:jpotoff_at_wayne.edu>
> Associate Professor and Director of Early Engineering Programs
> Department of Chemical Engineering and Materials Science
> Wayne State University 5050 Anthony Wayne Dr
> Detroit, MI 48202
> http://potoff1.eng.wayne.edu
> ==============================__==============================__==========
>
>
>
>
>
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