Except that since gbsa=0 in the output, the surface area calculation is not
done and not included in the forces. It is just telling you the default
surften value, but it does not use it here.
On May 15, 2015 5:08 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
> On Thu, May 14, 2015 at 11:46 PM, Huang <huangloligo.gmail.com> wrote:
>
> > I've run a simple MD with such an input:
> > =============================================
> > EQUILIBRATION
> > &cntrl
> > ntt=3, gamma_ln=5.0, ig=-1,
> > nscm=1000, igb=5,
> > saltcon=0.1, ntwx=1000, ntpr=100, temp0=298.0,
> > nstlim=10000,rgbmax=20.0,cut=22.0,
> > /
> > &wt
> > TYPE='END',
> > /
> >
>
> Is there any reason you're using a 22 A cutoff instead of an effectively
> infinite one (like 1000)? For implicit solvent calculations, an infinite
> cutoff is usually better.
>
>
>
> > =============================================
> >
> > and I find the output:
> > =============================================
> > Potential function:
> > ntf = 1, ntb = 0, igb = 5, nsnb =
> > 25
> > ipol = 0, gbsa = 0, iesp = 0
> > dielc = 1.00000, cut = 22.00000, intdiel = 1.00000
> > saltcon = 0.10000, offset = 0.09000, gbalpha= 1.00000
> > gbbeta = 0.80000, gbgamma = 4.85000, surften = 0.00500
> > rdt = 0.00000, rgbmax = 20.00000 extdiel = 78.50000
> > alpb = 0
> > =============================================
> >
> > Does it mean SASA of GBSA is calculated with surften=0.00500? With LCPO
> > method?
> >
>
> Yes.
>
>
> >
> > If I use the result mdcrd to run MMPBSA.py, should I keep using LCPO
> >
> > and surften=0.00500?
> >
>
>
> Seems like a good idea to me.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> 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 Fri May 15 2015 - 03:30:05 PDT
