VMD-L Mailing List

From: Nilesh Ingle (nileshingle_at_gmail.com)
Date: Thu Oct 08 2009 - 21:58:50 CDT

Thanks a lot John, Leandro !
Just to keep you posted, after updating the vmd to latest Aug09 release, it
came with a plugin called "Inorganic Builder" that too worked to create the
SiO2 monolayer.

Best Regards,
Nilesh.

On Tue, Oct 6, 2009 at 2:16 PM, daniel aguayo <bioquimico_at_gmail.com> wrote:

> I know a group working on packmol wrapper
>
> http://code.google.com/p/molecv1/
>
>
>
>
> On Tue, Oct 6, 2009 at 7:16 AM, Leandro Martínez <
> leandromartinez98_at_gmail.com> wrote:
>
>>
>> Hi John,
>>
>> Yes, I thought about it many times, I just didn't have the time
>> to do it. I also interchanged some e-mails with Axel Kohlmeyer
>> about this as well, he suggested that it may be interesting
>> to cuda-accelerate the package so that the box building could
>> be done on-the-flight, but this would be a next step. Whenever
>> I got sime time I will certainly try to do the VMD plugin.
>>
>> Best regards,
>> Leandro.
>>
>>
>>
>>
>>
>> On Mon, Oct 5, 2009 at 10:54 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>
>>>
>>> Leandro,
>>> I read your Packmol paper several months ago and found it rather
>>> interesting. Have you guys ever thought about wrapping it with a
>>> VMD plugin?
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Mon, Oct 05, 2009 at 09:24:44PM -0300, Leandro Martínez wrote:
>>> > Hello Nielsh,
>>> >
>>> > You may want to try the Packmol package:
>>> >
>>> > http://www.ime.unicamp.br/~martinez/packmol>
>>> >
>>> > Regards,
>>> > Leandro.
>>> >
>>> > On Mon, Oct 5, 2009 at 8:55 PM, Nilesh Ingle <nileshingle_at_gmail.com
>>> >
>>> > wrote:
>>> >
>>> > Hello Everybody,
>>> > I am trying to learn VMD for my project. And I need help with the
>>> > following,
>>> > How to create a monolayer (500Ao by 500Ao :: x by y, length and
>>> width)
>>> > using a couple of lysine (say) molecule. The thicknes of the layer
>>> would
>>> > be the thickness imparted by the lysine molecule.
>>> > I appreciate your time and kind attention. Thank You.
>>> > Best Regards,
>>> > Nilesh.
>>>
>>> --
>>> NIH Resource for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>>> WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/> Fax: 217-244-6078
>>>
>>
>>
>
>
> --
> saludos desde el fin del mundo
>