RE: DCD

From: Buddhadev Maiti (bmaiti_at_gsu.edu)
Date: Thu Apr 05 2012 - 16:22:52 CDT

Dear Gianluca,

Sorry for my unclear email. My dcd file is very big 30GB and if I try to open, my computer freezes. That is why I am searching some tcl script to strip water and ions. Could you please help me.
Have a nice day,
Thanks,
Maiti
________________________________________
From: Gianluca Interlandi [gianluca_at_u.washington.edu]
Sent: Thursday, April 05, 2012 5:04 PM
To: Buddhadev Maiti
Cc: Jérôme Hénin; namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: DCD

Load your psf+dcd into VMD. Choose File -> Save Coordinates. In the text
field you can enter your atom selection, e.g., "not (water or ions)"

Gianluca

On Thu, 5 Apr 2012, Buddhadev Maiti wrote:

> Dear Jerome,
>
> I would like to make new dcd file from original dcd file (protein +
> membrane + water + ion) including only protein and membrane part without
> including any water and ions. Could you please reply me if there is any
> vmd tcl utilities, it will be great help for me. I am working with psf
> and dcd files.
>
> Have a nice day,
> Thanks,
> Maiti
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:51 CST