----- Original Message -----
From: Birgit Hischenhuber <birgit.hischenhu...@meduniwien.ac.at>
Date: Wednesday, June 2, 2010 0:44
Subject: [gmx-users] Visualizing of a peptide in a water box - using trjconv
To: gmx-users@gromacs.org


         <!--  /* Style Definitions */  p.MsoNormal, li.MsoNormal, 
div.MsoNormal        {margin:0cm;    margin-bottom:.0001pt;  font-size:12.0pt;  
     font-family:"Times New Roman";} a:link, span.MsoHyperlink       
{color:blue;    text-decoration:underline;} a:visited, 
span.MsoHyperlinkFollowed        {color:purple;  text-decoration:underline;} 
span.E-MailFormatvorlage17  {mso-style-type:personal-compose;       
font-family:Arial;      color:windowtext;} @page Section1       {size:595.3pt 
841.9pt;  margin:70.85pt 70.85pt 2.0cm 70.85pt;} div.Section1     
{page:Section1;} -->   
-----------------------------------------------------------
| 

  
  > Hi,
  >  
  > I simulate a peptide in a water box with some ions to get a neutral 
solution. I want to visualize the peptide in the water box.
  > I want that the peptide is in the center of the box, but also have a look 
at the water.
  >  
  > Therefore I tried two things:
  >  
  > trjconv –f a.trr –o b.xtc –s c.tpr –skip 10 –pbc mol –ur compact –center 
–fit progressive
  >  
  > Visualizing it with VMD I see the peptide centering in the middle of the 
box, but the water get during the time holes.
  >  
  > So I checked the mailing list and find some inputs and tried it with two 
steps:
  >  
  > trjconv –f a.trr –o b.xtc –s c.tpr –pbc mol –ur compact
  > trjconv –f b.xtc –o d.xtc –s c.tpr –skip 10 –center –fit progressive
  

I don't think -ur or -fit are useful for your problem. I suspect something like 



trjconv -center

trjconv -pbc mol


is what you want, perhaps even in one pass. Obviously, check trjconv -h for 
info - it suggests the combination of the above...


Mark



  > at this try I get a peptide in the center of the box and during the time 
the pepide moves to the edge of the box and I consider that the box rotate 
around the peptide.
  >  
  > Is there a possibility that my peptide stays in the center of the box and 
the water doesn’t get any holes?
  >  
  > Thanks a lot for your helps!
  >  
  > ---
  >  
  > DI Birgit Hischenhuber
  > Unit for Medical Statistics and Informatics 
  > Section for Biomedical Computersimulation and Bioinformatics
  >  
     |
-----------------------------------------------------------
   > -- 
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search 
> before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


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

Reply via email to