VMD-L Mailing List

From: Anna (mol.dynamics_at_yahoo.com)
Date: Wed Aug 24 2011 - 15:12:02 CDT

Thank you , Mr Stone, for both this clarification and for your help with my rotation problem!

On 24 Aug 2011, at 21:08, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> If you get failed delivery messages, it is usually because one or more
> VMD-L members email addresses had a failed delivery. This is not unusual
> given that there are over a thousand subscribers. I got both of your posts,
> so there was certainly no delivery problem here. :-)
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Aug 24, 2011 at 08:53:46PM +0100, Anna wrote:
>> I apologise for repeated messages to the vmd list, but it always says that
>> my message cannot be delivered and I get a mailer daemon message saying I
>> tried, but ... So I gave up. Is this only me or do other members get this
>> as well?
>>
>> On 24 Aug 2011, at 18:34, Anna <mol.dynamics_at_yahoo.com> wrote:
>>
>> Begin forwarded message:
>>
>> From: Anna <mol.dynamics_at_yahoo.com>
>> Date: 24 August 2011 17:48:38 GMT+01:00
>> To: VMD list <vmd-l_at_ks.uiuc.edu>
>> Subject: Initial configuration reorientation
>>
>> Dear vmd developers/users!
>> I need to orientate cylinder-shaped polymers in order to simulate
>> them with LAMMPS, and I was given data for their initial orientation
>> and position from other experiments.
>> I have the following information: the coordinate (r) centre and
>> orientation vector (n) of long axis.
>> chain one: r1_x; r1_y; r1_z; n1_x; n1_y; n1_z
>> chain two: r2_x; r2_y; r2_z; n2_x; n2_y; n2_z
>> chain 1: -0.8; -2.1; 0.5; -0.07; 0.8; 0.5
>> chain 2: 2.6; 1.9; -2.2; -0.08; 0.9; 0.4
>> I am confused as to how I can approach this problem using vmd.
>> Thank you in advance for any input!
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078