On Mon, Aug 29, 2011 at 1:24 PM, Qin Zhang <zqyork.gmail.com> wrote:
> Dear All Amber users;
> I would like to take an energy minimization only based on GB energy,
> even though the energy model is not right. So I select ntf=8.
> But it still reports VDWAALS and EEL energy.
>
That's because VDW, EEL, and EGB are all non-bonded interactions. You can
zero out the VDW interactions by hacking the prmtop and setting every single
ACOEF and BCOEF term equal to zero. However, decoupling the EEL and EGB
calculations is impossible without hacking the code. However, I wouldn't
exactly consider EEL and EGB to be separate terms. You can arrange the GB
energy equation as a sum of terms in which one term takes the form of
gas-phase electrostatic interactions. This is how Amber "decomposes" the
electrostatic energy into an EEL term and an EGB term, but make sure you
know exactly what you want here.
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -1.2636E+04 4.6321E+00 4.2128E+01 NH2 1969
>
> BOND = 0.0000 ANGLE = 0.0000 DIHED =
> 0.0000
> VDWAALS = -1154.8397 EEL = -8971.0206 EGB =
> -2510.0640
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
>
> when I tried ntf=7. The results are exactly the same. When I check the code
> force.f in /src/sander, there seems no ntf<8 choice. Could you please
> point
> to me whether I can only select GB force for energy minimization? Or you
> can
> paste a right input file?
> My input is as follows.
>
> GB energy minimization
> &cntrl imin=1, maxcyc=10
> cut=300.0, igb=1, saltcon=0, gbsa=0, extdiel=80.0, intdiel=1.0
> ntpr=1, ntx=1, ntb=0, ntf=8
> &end
> &end
>
You do not need the second &end here. Also, I'm curious about why you do
not set ntc=3 in this case. If you don't evaluate any internal potential
terms, why aren't you constraining the length of every bond in the system?
It would seem to me that you would need to in order to preserve the
structure of your system and avoid getting nonsense (but I've never tried it
so I don't know).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Aug 29 2011 - 13:00:02 PDT
