Re: Annealing process of silica with excluded block

From: Marzieh Alishahi (alishahi.mar_at_gmail.com)
Date: Mon Sep 15 2014 - 09:40:21 CDT

Hi Jeff,

Thanks for your reply. I get what you mean by "wrapAll" and periodic
boundary condition. The only solution that I've found so far, is defining
restrain potential for all silica atoms located on the surface of solid
volume.

Best,
Marzieh

On Mon, Sep 15, 2014 at 7:09 PM, Marzieh Alishahi <alishahi.mar_at_gmail.com>
wrote:

> Hi Jeff,
>
> Thanks for your reply. I get what you mean by "wrapAll" and periodic
> boundary condition. The only solution that I've found so far, is defining
> restrain potential for all silica atoms located on the surface of solid
> volume.
>
> Best,
> Marzieh
>
> On Mon, Sep 15, 2014 at 7:00 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
>
>> Hello Marzieh,
>>
>> "wrapAll" does not affect the physics of the system (except sometimes
>> for a few specialized NAMD features). When the Si and O atoms "pass
>> through the boundaries of the system", they only appear to do so. I
>> would suggest reading more about how periodic boundary conditions
>> work.
>>
>> Best wishes,
>> Jeff
>>
>> –––––––––––––––––––––––––––––––––––
>> Jeffrey Comer, PhD
>> Assistant Professor
>> Department of Anatomy and Physiology
>> College of Veterinary Medicine
>> Kansas State University
>>
>>
>> On Fri, Sep 12, 2014 at 10:22 AM, Marzieh Alishahi
>> <alishahi.mar_at_gmail.com> wrote:
>> > Dear NAMD users,
>> >
>> > I want to perform “Annealing” process on a silica (Silicon Dioxide)
>> solid
>> > material which was primarily created by Inorganic Builder toolbox on
>> VMD and
>> > the point is that the silica is a cube with a smaller cube cut out from
>> the
>> > upper corner. That means at the upper surface of silica, there is a
>> part of
>> > excluded volume, so I cannot use “wrapAll on” in my NAMD configuration
>> file.
>> > And if I turn off the “wrapAll” command, the silica molecules will pass
>> the
>> > boundaries during annealing process. I Also try adding restrain on
>> silica
>> > atoms, but it seems somehow meaningless since it will cancel all the
>> > movements of atoms during annealing. I would be so grateful if any one
>> could
>> > help me to solve this problem.
>> >
>> > Thanks in advance,
>> >
>> > Marzieh
>>
>
>

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