[gmx-users] LJ cut-off distance

[C. Batistakis]

Dear Mark

Of course I agree with you but some times general knowledge is better than just solving a specific problem :-)

In any case, many thanks for your answer and your time

Best Regards, Chrysostomos



--- Στις Παρ., 22/10/10, ο/η Mark Abraham <Mark.Abraham at anu.edu.au> έγραψε:

Από: Mark Abraham <Mark.Abraham at anu.edu.au>
Θέμα: Re: [gmx-users] LJ cut-off distance
Προς: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Ημερομηνία: Παρασκευή, 22 Οκτώβριος 2010, 18:27



  

    
  On 23/10/2010 2:08 AM, C. Batistakis wrote:
    
      
        
          
            Dear Justin

              

              Actually, what I want to do is to kill the attraction part
              of the LJ substrate-polymer interaction. So, I was
              thinking to put the cut-off equal the 1,12σ (point with
              the lowest energy). 

            
          
        
      
    
    

    Mentioning the real objective, as well asking about a form of its
    solution is often productive :-)

    

    
      
        
          
            

              Do you have any other idea how can I have only the
              repulsion part? 

              

              If not, can you suggest me a further reading about how to
              use tabulated potentials?

            
          
        
      
    
    

    http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
    and several places in the manual.

    

    I think you want to use energy group tables, and to modify the
    functional form for only substrate-polymer energy group.

    

    Mark

    

    
      
        
          
            

              -Many thanks, Chrysostomos

              

              --- Στις Παρ., 22/10/10, ο/η Justin A. Lemkul <jalemkul at vt.edu>
              έγραψε:

              

                Από: Justin A. Lemkul <jalemkul at vt.edu>

                Θέμα: Re: [gmx-users] LJ cut-off distance

                Προς: "Discussion list for GROMACS users"
                <gmx-users at gromacs.org>

                Ημερομηνία: Παρασκευή, 22 Οκτώβριος 2010, 17:51

                

                

                  

                  C. Batistakis wrote:

                  > Dear all

                  > 

                  > I have a system of polymer chains between 2
                  substrates. The substrates are FCC lattices consisting
                  of Lennard-Jones particles.  

                  > I would like to know if it’s possible to handle
                  individually the cut-off distances of the LJ
                  interactions in the system

                  > 

                  > For example, I would to use one cut-off distance
                  for the LJ interactions between the particles of the
                  substrate but a different cut-off distance for the LJ
                  interaction between the substrate and the polymers. Is
                  this possible?

                  > 

                  

                  No.  There can be only one value of rvdw.  If you want
                  custom potentials, you can use tabulated potentials,
                  but I don't think this directly addresses what you
                  want to do.

                  

                  -Justin

                  

                  > Many thanks in advance

                  > 

                  > Chrysostomos

                  > 

                  > 

                  

                  -- ========================================

                  

                  Justin A. Lemkul

                  Ph.D. Candidate

                  ICTAS Doctoral Scholar

                  MILES-IGERT Trainee

                  Department of Biochemistry

                  Virginia Tech

                  Blacksburg, VA

                  jalemkul[at]vt.edu | (540) 231-9080

                  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

                  

                  ========================================

                  -- gmx-users mailing list    gmx-users at gromacs.org

                  http://lists.gromacs.org/mailman/listinfo/gmx-users

                  Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
                  before posting!

                  Please don't post (un)subscribe requests to the list.
                  Use the www interface or send it to gmx-users-request at gromacs.org.

                  Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

                
              
            
          
        
      
      

    
    

  

-----Ακολουθεί συνημμένο-----

-- 
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101022/f058d031/attachment.html>