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
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Received on Fri May 15 2015 - 02:30:09 PDT
