VMD-L Mailing List

From: Marc Q. Ma (qma_at_oak.njit.edu)
Date: Mon May 08 2006 - 14:05:31 CDT

Hi guys,

Does NAMD write coordinates that are wrapped? I thought NO. My
recollection is that NAMD only uses wrapping as a technique to
calculate forces, and the DCD file output uses coordinates without
wrapping.

Please correct me if I am wrong.

Marc
On May 8, 2006, at 1:08 PM, dimka wrote:

> if you used "wrapWater on" option in your simulations, i suppose you
> can look at minmax of just water oxygens. This will probably give you
> more-or-less accurate box size.
>
> On 5/8/06, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
>> On Mon, 8 May 2006, Guo Zhi wrote:
>>
>> GZ> Well, my system is NPT. I want to use "measure minmax
>> [atomselect top
>> water]" to calculate the unit cell info in each frame, is this
>> recovery
>> method correct?
>>
>> no, your cell will always be too large since molecules will always
>> be wrapped as a whole.
>>
>>
>> ---------- Forwarded message ----------
>> From: Guo Zhi <gzgzgz_at_gmail.com>
>> Date: 2006-5-7 ÏÂÎç11:32
>> Subject: vmd-l: How to pick up the lost periodic information?
>> To: vmd-l_at_ks.uiuc.edu
>>
>> Hi, VMD users:
>> I forgot to include DCDunitCell option in my simulation. So
>> that it
>> seems that the dcd trajectory file does not include any periodic
>> information( when i ticked any of the checkbox of +X, -X, +Y, -
>> Y... none of
>> them works ), but i really want to see the movie with smooth
>> boundary
>> connected, is it still possible? How to do it?
>> What's more, how to select neighboring atoms that stride two periodic
>> boxes?
>>
>> no, that is currently not possible. you have to duplicate the
>> atom coordinates accordingly and the analyse.
>>
>> regards,
>> axel.
>>
>> --
>> ===============================================================
>> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://
>> www.cmm.upenn.edu
>> Center for Molecular Modeling -- University of Pennsylvania
>> Department of Chemistry, 231 S.34th Street, Philadelphia, PA
>> 19104-6323
>> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
>> 1-215-898-5425
>> ===============================================================
>> If you make something idiot-proof, the universe creates a better
>> idiot.
>>
>>
>