# Re: PBC only along the z axis.

From: Sridhar Kumar Kannam (srisriphy_at_gmail.com)
Date: Sat Jan 04 2014 - 18:25:28 CST

Thank you Subbarao and Dave.

Dave, PME needs PBC's in all three directions. So we need to specify the
cell Basis Vectors in all three directions.
So the solution is to put some vacuum in the directions where we don't
apply PBC as Subbarao has suggested.

Best,

On Sat, Jan 4, 2014 at 10:18 AM, David Hardy <dhardy_at_ks.uiuc.edu> wrote:

> Dear Sridhar,
>
> Just set
>
> cellBasisVector1 0 0 100
>
> and don't define the others, as they simply default to zero.
>
> Then you have periodicity along the one vector that you want.
>
> Best regards,
> Dave
>
>
> On Jan 3, 2014, at 12:18 AM, Subbarao Kanchi <ksubbu85_at_gmail.com> wrote:
>
> Hi Sridhar,
> It is required to specify three basis vector for PME
> calculations.you can put some vacuum in the directions of non periodic by
> providing extra box size than that of actual.
>
>
> Cheers,
> Subbarao Kanchi.
>
>
> On Fri, Jan 3, 2014 at 9:16 AM, Sridhar Kumar Kannam <srisriphy_at_gmail.com>wrote:
>
>> Hi All,
>>
>> This is a trivial question but I am unable to solve.
>> I have a fluid confined inside a nanotube. I want to apply the PBC only
>> along the Z-axiz to simulate an infinitely long tube. I don't want to apply
>> PBC along the X and Y directions. How do I do this using the cell basis
>> vectors ...
>>
>> The following lines are giving the error message -
>> FATAL ERROR: Used cellBasisVector3 without cellBasisVector1!
>> FATAL ERROR: Used cellBasisVector3 without cellBasisVector2!
>>
>>
>>
>> cellBasisVector1 0.0 0.0 0.0
>> cellBasisVector2 0.0 0.0 0.0
>> cellBasisVector3 0.0 0.0 100.0
>> cellOrigin 0.0 0.0 0.0
>>
>>
>> Thanks.
>>
>>
>>
>> --
>> Cheers !!!
>> Sridhar Kumar Kannam :)
>>
>>
>>
>>
>
> --
> David J. Hardy, Ph.D.
> Theoretical and Computational Biophysics
> Beckman Institute, University of Illinois
> dhardy_at_ks.uiuc.edu
> http://www.ks.uiuc.edu/~dhardy/
>
>

```--
Cheers !!!
Sridhar  Kumar Kannam :)
```

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