Probably TIP4P-D, having an extra point, is vulnerable because the "bond"
between this EP and the parent oxygen is special. I'm not well versed in
the formalities of the sander minimizer when it comes to things like extra
point conventions; I only know that there would have to be conventions and
they would rely heavily on the particular details of the underlying
parameter set.
Dave
On Mon, Aug 1, 2016 at 12:10 AM, Suguru ASAI <suguruasai.gmail.com> wrote:
> Dear David,
>
> Thanks for your suggestion and I'm sorry for late reply. It seems
> `ntc=2` fix the problem.
>
> But I'm wondering why only TIP4P-D requires this parameter while the
> Amber 14 manual said
>
> > Since SHAKE is an algorithm based on dynamics, the minimizer is not
> aware of what SHAKE is doing; for this
> > reason, minimizations generally should be carried out without SHAKE.
> One exception is short minimizations
> > showse purpose is to remove bad contact before dynamics can begin.
>
> Because of this, following my minimization steps were performed with
> default `ntc=1`:
>
> 1. Minimizeation of H atoms on the protein and solvent molecules (ntr=1,
> restraintmask='.N=,C=,O=,S=,Na=,Cl=')
> 2. Minimization of Na+, Cl- and solvent molecules (ntr=1,
> restraintmask=:<PROTEIN>)
> 3. Minimization of the system (ntr=0)
>
> And applying `ntc=2` at the initial step solve the problem.
> So is my case an exception or `ntc=2` should be performed for the
> initial minimization step generally?
>
>
> Thanks for taking time.
>
>
> Asai
>
> On 07/29/2016 07:46 AM, David A Case wrote:
> > On Thu, Jul 28, 2016, Suguru ASAI wrote:
> >> EEL value in mdout become ******* in minimization and a program failed.
> >> I would like to solve this problem but don't know where to check or how
> >> to fix.
> > Something bad is happening around atoms 560 and 570. Have you set ntc=2
> > in your input file? This is required for rigid water models. Otherwise
> > you can get hydrogens arbitrarily close to oxygens on neighboring
> molecules.
> >
> > ....dac
> >
> >
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>
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Received on Sun Jul 31 2016 - 22:30:02 PDT
