VMD-L Mailing List

From: Anna (mol.dynamics_at_yahoo.com)
Date: Wed Aug 24 2011 - 12:34:11 CDT

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!
>>
>>