This comes up with lipid simulations all the time, and as I recall the
answer has always been no.
E.g.
http://ambermd.org/tutorials/advanced/tutorial16/
" Your system will be rectangular and periodic in the X, Y, and Z
dimensions."
Bill
On 8/6/16 10:34 PM, Ming Tang wrote:
> Thank you Bill,
>
> Is it possible for me to apply constant pressure with periodic boundary condition along Z direction only, while keeping the four walls parallel to the Z-axis fixed. I want to apply this boundary because my protein is long and I plan to do SMD. If I use constant volume, the computational cost will be too huge.
>
>
> -----Original Message-----
> From: Bill Ross [mailto:ross.cgl.ucsf.edu]
> Sent: Sunday, 7 August 2016 11:59 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] How to fix the wall of the water box in amber
>
> To keep the box walls from moving, use constant volume (NVT).
>
> When adding waters in leap, it is normal to equilibrate at constant pressure before going to constant volume.
>
> Bill
>
>
> On 8/6/16 6:17 PM, Ming Tang wrote:
>> Dear list,
>>
>> Is there a way to fix the wall of the water box in amber?
>>
>> Thank you.
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Aug 07 2016 - 02:30:02 PDT
