VMD-L Mailing List

From: Kos (asimplefunguy_at_netscape.net)
Date: Fri Apr 22 2005 - 10:43:11 CDT

Hi,

about DCD_splitters I think that we should try CHARMM
or is there any other free suggestion please?
Bogdan please explain what do you mean about CHARMM problems by 'I/O bandwidth and passes' (examples HW)?

I think that in the past John Stone emphasized that for larger than 2GB files one needs 64bit environment(both hardware and OS?)
Our LINUX clusters are AMD dual K7 ATHLON and INTEL dual XEON (130nm,32bit)
so they don't support 64bit technology.
We bought recently an HP laptop ZD8000,17" with the new Intel chipset; 64bit technology (650 HT).Also Windows 64bit are available but even with Windows XP(32) could I use a version of VMD-win that supports 64bit machines?

Why there is not a VMD option to do only math-calculations eg RMS,g(r), torsion analysis (no graphics required)and then don't load graphically trajectories, pdb files
saving a lot of memory and enchance speed please?
Let's say only command line VMD-env.

Kos

Bogdan Costescu <Bogdan.Costescu_at_iwr.uni-heidelberg.de> wrote:

>
>On Thu, 21 Apr 2005, Kos wrote:
>
>> Is CHARMM an alternative solution to these problems and can treat
>> large files faster because doesn't need graphics?
>
>A bit simplified view is that CHARMM might not need much memory for
>analysis because it can load the trajectory frame by frame, so at any
>given time only one frame is in memory. The disadvantage is that it
>makes the analysis limited by the I/O bandwidth of the computer (to
>local disk or NFS server) when you want to do several passes through
>the whole trajectory; if you load the whole trajectory in RAM, it's
>much faster for the second or subsequent passes.
>

__________________________________________________________________
Switch to Netscape Internet Service.
As low as $9.95 a month -- Sign up today at http://isp.netscape.com/register

Netscape. Just the Net You Need.

New! Netscape Toolbar for Internet Explorer
Search from anywhere on the Web and block those annoying pop-ups.
Download now at http://channels.netscape.com/ns/search/install.jsp