Thank you Bill and Daniel (solvatebox mol TIP3PBOX {x y z}) for your
solutions. Both work perfectly.
The reason to do that is exactly to create less water molecules in the
system but to have a box long enough to pull one of the molecules
without moving it to the next periodic box in steered MD.
Regards,
Sergey
On 07/26/2011 07:52 PM, Bill Ross wrote:
>> 4. Is there the way in Leap to create an assymetric water box for PBC
>> with an elongated side, along which the pulling is occuring? This would
>> save the computational expenses a lot in case of SMD.
>>
> You could place an ion off to the side manually (either in xleap or
> externally + loadpdb), solvate, then delete the ion.
>
> Bill
>
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--
Sergey A. Samsonov
Postdoctoral researcher
Structural Bioinformatics
Biotechnology Center
Tatzberg 47-51
01307 Dresden, Germany
Tel: (+49) 351 463 400 83
Fax: (+49) 351 463 402 87
E-mail: sergey.samsonov.biotec.tu-dresden.de
Webpage: www.biotec.tu-dresden.de
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Received on Thu Jul 28 2011 - 03:00:04 PDT
