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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