Not to jinx it though using GAFF2 seems to have solved the most volatile problem as I have now managed to perform a temperature equilibration.
Thank you David
// Gustaf
> On 20 Jul 2019, at 13:51, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> Hello David
>
>
> As I am enjoying some days of work I will look into this as soon as I get back to the office. No, I am not using gaff2 though I will definitely give that a try and look into the angle constant to see what I can accomplish.
>
>
> Thank you for you tips and have a nice weekend
>
> // Gustaf
>
> ________________________________
> Från: David Case <david.case.rutgers.edu>
> Skickat: den 14 juli 2019 14:50:51
> Till: AMBER Mailing List
> Ämne: Re: [AMBER] Problem with Phenylphosphonic acid
>
> On Fri, Jul 12, 2019, Gustaf Olsson wrote:
>>
>> I am running three different systems that contain pehnylphosdhonic acid,
>> the neutral form (ppa) the anion (pp1) and the double negative anion
>> (pp2).
>
> I bet that one of the protons on the phosphorous is getting very close
> to one of the other phosphate oxygens. At least, this is a common
> problem with protonated phosphates, although it's not clear why ppa
> should be different than ppa1.
>
> Are you using gaff2? One of the important changes between gaff and
> gaff2 is that atom type "ho" is given non-zero van der Waals radii,
> which should prevent the hydrogen from getting too close to a
> neighboring oxygen. You may also need to increase (say double) the
> P-O-H angle constant.
>
> Since the problem happens quickly, run a short trajectory with ntwx=1 or
> 2, and visualize the geometry of the phopshate group as it gets close to
> the point where the system crashes.
>
> ...hope this helps...problem could be something different, of
> course....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 30 2019 - 04:00:03 PDT
