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 Fri Mar 22 2019 - 01:00:02 PDT
