Re: Fixed atoms.

From: Aron Broom (
Date: Thu Jun 05 2014 - 17:03:12 CDT

I don't think anyone uses a particular software, you're just changing a
text value. You just need to use a text editor that isn't garbage (or
probably most people write a quick python or bash script). I'm guessing
you are on Windows? There are windows versions of decent linux editors,
but there are also native-windows editors like
that are good editors that won't mangle the files.

You only change the beta values of the atoms you want to fix, so just only
change the carbon atoms beta-values... It almost sounds like you were
trying to change ALL the beta values, which would make for pretty static

But really, if you are in the business of doing MD, you should invest the
time in learning a simple scripting language, the most popular at the
moment being python, and then you can write some quick code to automate
this task for you. It's difficult to overstate the benefits of having at
least some minor coding ability and understanding.

On Thu, Jun 5, 2014 at 5:15 PM, Gurpreet Kaur Dhindsa <>

> Dear all,
> I want to fix atoms in my simulation. By reading the blogs, they said I
> have to change the
> 'B' value from 0 to 1 to fix the atoms. Can you please guide me what
> software can do this?
> I tried with textpad but it changed the format of pdb. The other thing, my
> system contains water
> and carbon. I want to fix carbon only. Please tell me what commands should
> I use to fix the
> carbon atoms.
> Thanks,
> G

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:26 CST