[gmx-users] Tetrahydrofuran OPLS-AA forcefield

[David van der Spoel]

On 2015-04-21 20:07, André Farias de Moura wrote:
> Hi Marie,
>
> Topologies are much of a handcraft: I just read the description of atoms
> types within the OPLSAA GROMACS file and those types just seemed to match
> the chemical classification of the atoms comprising THF. You just need to
> check if atomic charges add up to zero, because otherwise you might be
> assigning some wrong atom types. If you're still not confident about the
> choices you've made, run a pure liquid simulation and check some standard
> thermodynamic properties, for instance density and heat of vaporization.
>
> I hope it helps.
>
Here are files and some data for this compound:
http://virtualchemistry.org/molecule.php?filename=tetrahydrofuran.zmat

> best,
>
> Andre
>
> ps: please keep discussion within the list, so others may benefit from it
> as well.
>
>
> On Tue, Apr 21, 2015 at 1:51 PM, Marie Tritschel <MarieTritschel at gmx.de>
> wrote:
>
>>   Dear Mr Farias de Moura,
>>
>> my name is Marie Kathrin Tritschel and I am working on my master thesis at
>> the university in Bayreuth in the
>> Biofluid Simulation and Modeling research group. I am performing molecular
>> dynamic simulations of P3Ht chaines
>> dissolved in Tetrahydrofuran (THF).
>>
>> As I have already written my forcefied for the P3HT-chains with OPLS-AA I
>> would like to write a forcefield for
>> tetrahydrofuran (THF) with OPLS-AA now.
>>
>> I found your helpful answer to a question about that topic at:
>> https://www.mail-archive.com/gmx-users@gromacs.org/msg15983.html
>>
>> My question ist now: From where did you get those parameters for the THF -
>> OPLS-AA forcefield?
>>
>> I would be really glad to hear from you. Thank you in advance.
>>
>>
>> Yours sincerely,
>> Marie Kathrin Tritschel
>>
>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se