Re: A larger protein data bank for performance benchmark

From: linux freaker (
Date: Mon May 13 2013 - 21:02:59 CDT


I appreciate your response.
Actually I am into High Performance Computing Team where I need to
benchmark different kinds of processor family using NAMD.
I just installed it and able to see that running ./namd src/alanin took
0.0085 sec. It finishes up in no seconds.

As I am quite new, I need to know if I actually need to build it to supply
like alanin running directly like:

./namd2 src/x.pdb

just works or I need to build pdb format? Please suggest.

It would be great if you can send me one or two PDBs which are large in
size and should take sometime for namd to finish.
Also, it should run directly like ./namd2 src/?.pdb.

On Tue, May 14, 2013 at 7:22 AM, Rebecca Swett <>wrote:

> I think you are being somewhat unclear. Are you looking for the PDB
> structure of a large protein? or are you looking for a large set of PDB's?
> The acronym PDB stands for protein data bank, is the
> repository of known crystal structures. Used as a file extension, it
> represents
> crystallographic coordinates saved in the standardized protein data bank
> format. is where you would find most known structure files in
> the downloadable format
> of numbers and letters. For example 2aa1.pdb is the structure of the day
> today and is a large toxin. If you are looking for a collection of
> structure files in pdb format, you may want to look at some of the search
> and download options on that site. However I strongly suggest doing some
> more reading. It is imperative to good science that users understand the
> files and formats they are working with.
> R.J. Swett
> Wayne State University
> 357 Chemistry
> Detroit, MI 48201
> Lab Phone 313-577-0552
> Cell Phone 906-235-0768
> On 5/13/2013 8:51 PM, linux freaker wrote:
> Hi All,
> I looked into but couldnt get large size protein data bank. As I
> am new to NAMD, please suggest me larger PDB.
> is the link I
> tried looking into but those are samll size PDBs.
> Can you please paste the link for large size PDB?
> Also, is it possible to accomunlate and run ./namd2 src/* for selecting
> various PDBs?
> On Mon, May 13, 2013 at 11:42 PM, linux freaker <>wrote:
>> Which shall I choose? can you suggest me a pdb just like alanin which I
>> can use directly?
>> On 13 May 2013 22:43, "Ajasja Ljubetič" <>
>> wrote:
>>> Here is a ready to run benchmark (apo1)
>>> (Direct download<>
>>> )
>>> On 13 May 2013 18:52, Cesar Millan <> wrote:
>>>> On Mon, May 13, 2013 at 11:49 AM, linux freaker <
>>>> > wrote:
>>>>> I installed namd on linux machine.I ran src/alanin on 4 processor and
>>>>> it completed in no time.I need it to take some 5-10 minutes running so that
>>>>> I can benchmark.where I can download pdb from which is larger in size?

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