> is that what's suppose to happen?
That's what the big mucky-mucks decide, and they don't talk to me.
On 3/25/19 8:28 AM, Charles Lin wrote:
> So I just looked through the code, the code simply just takes efx, efy, efz and multiplies the charge and accumulates that into the force accumulators for the variables.
>
> In terms of your comment about it being in a cyclic manner is that what's suppose to happen?
>
> I'll take a deeper dive into this next week.
>
> On 3/22/19, 3:40 AM, "Bill Ross" <ross.cgl.ucsf.edu> wrote:
>
> If you tell it what it wants to hear for the result you want, do things
> look reasonable otherwise? You could read the code now to convince
> yourself it's a mere input transposition, or you could just run while
> waiting to see if someone with more of a stake can clarify. I'm just the
> janitor, I hardly ever operate on patients. :-)
>
>
> On 3/21/19 11:48 PM, Ashutosh Mishra wrote:
> > I tried to apply along x and y direction also. I got similar results. For
> > electric field along z direction the dipole was along y. For field along y
> > direction the dipole was along x and for field in x it was along z (in a
> > cyclic manner).
> >
> > On Fri, Mar 22, 2019 at 12:15 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> My bad since new feature to me.
> >>
> >> What if you try the x or y axis, and see if the resulting axis implies
> >> anything?
> >>
> >> On 3/21/19 11:43 PM, Ashutosh Mishra wrote:
> >>> Production
> >>> &cntrl
> >>> imin = 0,
> >>> nmropt = 0,
> >>> ntx = 5,
> >>> irest = 1,
> >>> ntxo = 2,
> >>> ntpr=500, ntwx=500, ntwe=500, ntwr=500,
> >>> ioutfm = 1,
> >>> ntf=2, ntb=1,
> >>> ntave=1000,
> >>> ntr = 1,
> >>> nstlim = 2000000,
> >>> dt = 0.001,
> >>> ntt = 1,
> >>> tempi = 300, temp0 = 300,
> >>> tautp=0.5,
> >>> cut = 9.0,
> >>> ntp = 0,
> >>> pres0 = 1.0,
> >>> ntc = 2,
> >>> efz = 5.1085
> >>>
> >>>
> >>> This is the input file I used. To apply the electric field I used the
> >>> command "efz = 5.1085".
> >>>
> >>> On Fri, Mar 22, 2019 at 12:11 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> >>>
> >>>> How did you apply the field? Can you show input, or code if added?
> >>>>
> >>>> Bill
> >>>>
> >>>> On 3/21/19 11:26 PM, Ashutosh Mishra wrote:
> >>>>> I doing a simulation using AMBER18. In that simulation I had applied an
> >>>>> electric field along z direction, but strangely when I analyze the
> >>>>> trajectory I find that the dipole moment is aligning along y direction.
> >>>>> This is what my input file looks like.
> >>>>>
> >>>>> Production
> >>>>> &cntrl
> >>>>> imin = 0,
> >>>>> nmropt = 0,
> >>>>> ntx = 5,
> >>>>> irest = 1,
> >>>>> ntxo = 2,
> >>>>> ntpr=500, ntwx=500, ntwe=500, ntwr=500,
> >>>>> ioutfm = 1,
> >>>>> ntf=2, ntb=1,
> >>>>> ntave=1000,
> >>>>> ntr = 1,
> >>>>> nstlim = 2000000,
> >>>>> dt = 0.001,
> >>>>> ntt = 1,
> >>>>> tempi = 300, temp0 = 300,
> >>>>> tautp=0.5,
> >>>>> cut = 9.0,
> >>>>> ntp = 0,
> >>>>> pres0 = 1.0,
> >>>>> ntc = 2,
> >>>>> efz = 5.1085,
> >>>>>
> >>>>> can you suggest me what may be wrong in this simulation.
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Received on Mon Mar 25 2019 - 12:30:02 PDT
