VMD-L Mailing List

From: Samuel Coulbourn Flores (scflores_at_stanford.edu)
Date: Wed Dec 16 2009 - 09:59:47 CST

Hi Guys,

I am trying to hide one chain in my molecule, chain z. However if I type "not chain z" in the "Selected Atoms" box, I get an error saying, "The atom selection you typed could not be understood." It seems to understand other chain ID's, even lowercase ones. I guess I could rename the chain in the input file, but it breaks up the nice scheme I had worked out for handling multiple ribosomes without running out of alphanumeric characters for chain IDs. Presumably this is a bug. Is there a workaround?

Thanks

Sam

----- Original Message -----
From: "Berit Hinnemann" <behi_at_topsoe.dk>
To: "VMD" <vmd-l_at_ks.uiuc.edu>
Sent: Wednesday, December 16, 2009 7:16:14 AM GMT -06:00 US/Canada Central
Subject: Re: vmd-l: Graphics card for VMD

Dear all,

Thank you very much for your input and recommendations. I am right now checking prices with our IT department, and you gave me good grounds for making a decision.

Best regards, Berit

Berit Hinnemann
Research Scientist | Characterization Department | Research and Development Division

Haldor Topsøe A/S
Catalysing your business
Nymøllevej 55, DK-2800 Kgs. Lyngby
Phone: +45 4527 2130 (direct)

Read more at www.topsoe.com

        Axel Kohlmeyer <akohlmey_at_gmail.com>
Sent by: owner-vmd-l_at_ks.uiuc.edu

15-12-2009 21:19
                
To Berit Hinnemann <behi_at_topsoe.dk>
        
cc VMD <vmd-l_at_ks.uiuc.edu>
        
        
        
Subject Re: vmd-l: Graphics card for VMD
                

On Tue, 2009-12-15 at 18:25 +0100, Berit Hinnemann wrote:
> Dear all,
>
> I am planning to buy a new computer, which is to be used for VMD
> visualizations. I previously had an nvidia GeForce graphics card, and
> I would like to choose that again. Which model would you recommend
> that works well with vmd 1.8.7, and also can use the new acceleration
> features? I am planning to run RHEL 5 on the machine. Other than that,
> a quad core processor and 8GB memory I think.

whatever you can afford. at GTX 285 is currently the top performing
card and will also help a lot in the GPU accelerated computing modules.

i would look for a model that doesn't aggressively overclock and
has solid cooling and thus makes less noise, which i consider
important in a desktop.

the quadro cards are _much_ more expensive but required in case you
need stereo. i am very happy with the GTX285 in my desktop which
had replaced a mid-level (pre-CUDA) quadro card (which wasn't bad
for visualization with GLSL either).

the GTX 295 is the top model, but it is basically two GTX 260 cards
rolled into one case. that would allow you to e.g. have one GPU
dedicated for graphics and one for GPU computing. but then again,
it depends on your typical usage patterns, how much you'd gain
from it. if you want to spend less money, you can reduce your
requirements to, say, a GTX 280, GTX 275, GTX 260 perhaps even
a GTX 250.
if you want to have a single slot card, there are 9800 series
cards, which are also much less power hungry, but they are one
compute architecture older (yet, the fastest 9800 series card
is still at about 50% the speed of the fastest cards).

HTH,
axel.

> I would appreciate any recommendations. Thanks!
>
> Best regards,
> Berit
>
> ______________________________________________________________________
>
> Berit Hinnemann
> Research Scientist | Characterization Department | Research and
> Development Division
>
> Haldor Topsøe A/S
> Catalysing your business
> Nymøllevej 55, DK-2800 Kgs. Lyngby
> Phone: +45 4527 2130 (direct)
>
> Read more at www.topsoe.com
>
>
> ______________________________________________________________________
>
>
> This e-mail message (including attachments, if any) is confidential
> and may be privileged. It is intended only for the addressee.
> Any unauthorised distribution or disclosure is prohibited. Disclosure
> to anyone other than the intended recipient does not constitute waiver
> of privilege.
> If you have received this e-mail in error, please notify the sender by
> e-mail and delete it and any attachments from your computer system and
> records.
> HALDOR TOPSOE ( www.topsoe.com ) 

-- 
Dr. Axel Kohlmeyer akohlmey_at_gmail.com 
Institute for Computational Molecular Science 
College of Science and Technology 
Temple University, Philadelphia PA, USA. 
This e-mail message (including attachments, if any) is confidential and may be privileged. It is intended only for the addressee. 
Any unauthorised distribution or disclosure is prohibited. Disclosure to anyone other than the intended recipient does not constitute waiver of privilege. 
If you have received this e-mail in error, please notify the sender by e-mail and delete it and any attachments from your computer system and records. 
HALDOR TOPSOE ( www.topsoe.com )