VMD-L Mailing List

From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Mon Nov 01 2010 - 21:40:11 CDT

Hi Jerome,

Thanks for your reply. I really found your comments useful.
Before writing any script to work on my own PC (second method as you mentioned), I would prefer to use the VMD text mode and use the command:

vmd -dispdev text -e script.tcl

I found the pbcunwrap.tcl script as provided in pbctools 2.5. However, after typing

vmd -dispdev text -e pbcunwrap.tcl

this is what I get:

Info) VMD for LINUXAMD64, version 1.8.7a63 (March 31, 2009)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 8 CPUs detected.
Info) Free system memory: 7613MB (95%)
Info) No CUDA accelerator devices found.
Info) Creating CUDA device pool and initializing hardware...
vmd >

It seems that vmd does not do anything. I think it does not even start loading the psf and dcd files. So, I tried this:

vmd -dispdev text -psf filename.pdf -dcd filename.dcd

and it loads both files successfully. Then I tried running pbcunwrap.tcl using several guessed commands but, none of them worked. Would you please help me if you have any idea?

Thanks,
Parisa

-----Original Message-----
From: heninj_at_gmail.com on behalf of Jérôme Hénin
Sent: Mon 11/1/2010 6:12 AM
To: Parisa Akhski
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: VMD text mode/unwrap
 
Hi Parisa,

On 1 November 2010 01:53, Parisa Akhski <Parisa.Akhshi_at_chem.queensu.ca> wrote:
> Dear VMD users,
>
> I have two questions and would really appreciate if anyone could help me:
> 1. I have done a MD simulation in three restart jobs. I would like to first
> load all dcd files after each other to save
> all trajectory files (dcd files) as one dcd file. Then, I want to unwrap the
> whole system. The problem is that I cannot use VMD on my PC (windows/
> Ubuntu) to load more than 7000 frames while I have overal 100000 frames.
> My guess is that I may be able to do this using super computers but, I don't
> know where I can find the commands for text mode VMD on Unix. Is there any
> document which can provide me with this information?

If your script is in file script.tcl, type:
vmd -dispdev text -e script.tcl

(you can add the command "exit" at the end of the script if you want
VMD to terminate and return to the command line after running it)

> 2. Since I have an idea of which frames I would like to study for now, I can
> only load those frames on my own PC.
> But, I realized that to unwrap the system if I don't start from the first
> frame, the results of unwrap don't seem to be correct. I am wondering how
> unwrap works (I mean does it take the coordination of the system for the
> first frame and unwraps all system for the next frames with respect to the
> first one?) If so, I can only load the first frame and the ones I need to
> unwrap without the need to load the whole trajectory files.

Unwrap uses the first frame as a reference for the second one, then it
uses the unwrapped second frame as a reference for the third, and so
on. It relies on the fact that each frame is fairly similar to the
previous one.

If you want to process the trajectory on your desktop, you could write
a script that does the following:
a) load as many frames as will fit in memory (say, 0 to 7000)
b) run unwrap
c) save frames to new DCD file
d) delete all frames but the last one (0 to 6999) - keep the last
(7000) as a reference
e) load frames 7001 to 14000
f) run unwrap
g) save all but the first frame (7001-14000) to new DCD file

Repeat steps d) to g) until the whole trajectory has been unwrapped,
then possibly use catDCD to repackage the unwrapped frames into a
different number of DCD files.

Best,
Jerome