Periodicity is all or nothing, I believe.
Bill
On 6/6/17 11:59 PM, Jianing Song wrote:
> Thanks very much, Charlie.
>
> A secondary membrane protein always uses the electrochemical potential to transports substrate into cells. If I add an external electric filed along Z axis, Should I turn off the periodicity of the simulation box in Z axis?
> Since the periodicity of the simulation box in Z axis will cause the ineffectively of the external electric filed in Z axis.
>
> Best,
> Jianing
>
>
>
>
>
> On 7 Jun 2017, at 14:21, Charles Lin <clin92.ucsd.edu<mailto:clin92.ucsd.edu>> wrote:
>
> The periodicity for the electric field is for how often it fluctuates not for the periodicity of the simulation box. Currently there's no way to set periodicity in certain directions. To turn off x and y directions for your efield just set efx=0 and efy=0.
>
>
> Charlie
> ________________________________
> From: Jianing Song <sjn_sk.hotmail.com<mailto:sjn_sk.hotmail.com>>
> Sent: Wednesday, June 7, 2017 12:49:45 AM
> To: amber.ambermd.org<mailto:amber.ambermd.org>
> Subject: [AMBER] External electric fields support for GPU and how to set the parameters in mdin files?
>
> Dear all,
>
> Would you please tell me whether AMBER16 supports external electric fields in GPU now?
>
> I want to simulate a membrane protein located in a lipid bilayer, and try to add external electric field only to the Z axis. Then the periodicity of the system should be only set to X and Y axis, not Z axis, Is this right?
> If right, would you please tell me how to set the parameters efphase and effreq in the mdin files?
>
> Thanks very much.
>
> Jianing
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Received on Wed Jun 07 2017 - 00:30:03 PDT
