VMD-L Mailing List

From: hamid mosaddeghi (hamid592004m_at_yahoo.com)
Date: Fri Jan 18 2013 - 03:16:37 CST

Dear Mrs Alishahi   about Cutoff, I am agree with you but about Basis vectors , please see example of vmd :   au.pdb is: ---------------- ATOM      1 AU1  AU  X   1       0.000   0.000   0.000  1.00  0.00      UC1 AU 0 ATOM      2 AU2  AU  X   1       0.000   2.039   2.039  1.00  0.00      UC1 AU 0 ATOM      3 AU3  AU  X   1       2.039   0.000   2.039  1.00  0.00      UC1 AU 0 ATOM      4 AU4  AU  X   1       2.039   2.039   0.000  1.00  0.00      UC1 AU 0 END ----------------  and basis vectors are:              { 4.0782    0   0 }            { 0   4.0782    0 }            { 0   0   4.0782 }    cutoff 2.9    according your comment, basis vector should be:              { 2.039   0   0 }            { 0   2.039    0 }            { 0   0   2.039 }   please for more information, see other example as Si,...   thanks ----- Forwarded Message ----- From: Marzieh Alishahi <alishahi.mar_at_gmail.com> To: hamid mosaddeghi <hamid592004m_at_yahoo.com> Cc: vmd <vmd-l_at_ks.uiuc.edu> Sent: Friday, 18 January 2013, 10:21 Subject: Re: vmd-l: about inorganic builder and define variable hi  try your Basis vectors as follows; 1.4440.00.0 0.04.1700.0 0.00.04.718 about Cutoff, I think it can be defined according to Bond distance between AG atoms. Best, Marzieh Alishahi On Fri, Jan 18, 2013 at 1:49 AM, hamid mosaddeghi <hamid592004m_at_yahoo.com> wrote: Dear VMD users > >I need to add new material to inorganic builder. > >but I have problem with define cutoff and Basis vetors. > >for exmaple I want to add silver to it. I prepare proper *.pdb and *.top file for it. > >my pdb of unit cell is: > >------------------------------------------------------------------------------------------- >ATOM      1 AG1  AG  X   1       0.000   0.000   0.000  1.00  0.00      UC1 AG 0   >ATOM      2 AG2  AG  X   1       1.444   2.502   0.000  1.00  0.00      UC1 AG 0   >ATOM      3 AG3  AG  X   1       0.000   1.668   2.359  1.00  0.00      UC1 AG 0   >ATOM      4 AG4  AG  X   1       1.444   4.170   2.359  1.00  0.00      UC1 AG 0   >ATOM      5 AG5  AG  X   1       1.444   0.834   4.718  1.00  0.00      UC1 AG 0   >ATOM      6 AG6  AG  X   1       0.000   3.336   4.718  1.00  0.00      UC1 AG 0 >END >----------------------------------------------------------------------------------------------- > >for this pdb file how define proper Basis vetors and Cutoff? > >thnaks for attention > >Hamid Mosaddeghi > >Phd Student Of Physical Chemistry