From: Anna Borlsky (annanamd_at_gmail.com)
Date: Sat Feb 15 2014 - 04:34:49 CST
Dear Kenno and other members of namd mailing list,
Is it coumarin. I am planning at the begining only to simulate coumarin
alone to see if it was well parameterized. The topology and the parameter
files were generated by xplo2d and are in xplor format. Please find
attached the files.
Kind regards,
Anna
2014-02-14 1:48 GMT+00:00 Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu>:
> 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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