Re: simulation box

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri May 20 2011 - 11:33:20 CDT

2011/5/20 PAUL NEWMAN <paulclizana_at_gmail.com>:
> Hello,
> I want to set up the size of my simulation box and also center my protein.
> Let's say in x=100; in y=200 and z=50. How can I do that by using the
> commands inside NAMD like solvate.

solvate is not a NAMD command.

axel.

> Thanks
>
> On Fri, May 20, 2011 at 12:25 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Fri, May 20, 2011 at 12:11 PM, PAUL NEWMAN <paulclizana_at_gmail.com>
>> wrote:
>> > Thanks for the information; but are there any other way using just the
>> > commands inside NAMD.
>>
>> paul,
>>
>> your question is not very clear.
>>
>> you have to explain in more detail as to what
>> commands exactly you are referring to and
>> what it is exactly that you want to different and why.
>>
>> please reformulate your question and your
>> chances of getting a useful answer will improve.
>>
>> cheers,
>>    axel.
>>
>>
>>
>> > Thanks
>> >
>> > 2011/5/20 Marek Maly <marek.maly_at_ujep.cz>
>> >>
>> >> Hi,
>> >> I am not an expert on NAMD (I am AMBER user) but one alternative for
>> >> you
>> >> might be to create your simul. box outside for example using PACKMOL
>> >>
>> >> http://www.ime.unicamp.br/~martinez/packmol/
>> >>
>> >> Best,
>> >>
>> >>   Marek
>> >>
>> >>
>> >>
>> >> Dne Fri, 20 May 2011 17:39:48 +0200 PAUL NEWMAN <paulclizana_at_gmail.com>
>> >> napsal/-a:
>> >>
>> >>> Hi,
>> >>> I would like to know how to set up the size of the simulation box in
>> >>> NAMD. I
>> >>> want to set up X Y and Z. I dont want to use the one give by NAMD
>> >>>
>> >>> Thanks for the help
>> >>>
>> >>> Paul
>> >>>
>> >>>
>> >>>
>> >>> __________ Informace od ESET NOD32 Antivirus, verze databaze 6138
>> >>> (20110520) __________
>> >>>
>> >>> Tuto zpravu proveril ESET NOD32 Antivirus.
>> >>>
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>> >>
>> >>
>> >> --
>> >> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>> >> http://www.opera.com/mail/
>> >
>> >
>> >
>> > --
>> > Cheers,
>> >
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer
>> akohlmey_at_gmail.com  http://goo.gl/1wk0
>>
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.
>
>
>
> --
> Cheers,
>
> Paul
>
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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