Re: A larger protein data bank for performance benchmark

From: linux freaker (linuxfreaker_at_gmail.com)
Date: Mon May 13 2013 - 19:51:51 CDT

Hi All,

I looked into pdb.org but couldnt get large size protein data bank. As I am
new to NAMD, please suggest me larger PDB.
http://chemistry.gsu.edu/Glactone/PDB/Amino_Acids/aa.html 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 <linuxfreaker_at_gmail.com>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" <ajasja.ljubetic_at_gmail.com> wrote:
>
>> Here is a ready to run benchmark (apo1)
>> http://www.ks.uiuc.edu/Research/namd/performance.html (Direct download<http://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz>
>> )
>>
>>
>>
>>
>>
>>
>> On 13 May 2013 18:52, Cesar Millan <pachequin_at_gmail.com> wrote:
>>
>>> www.pdb.org
>>>
>>>
>>> On Mon, May 13, 2013 at 11:49 AM, linux freaker <linuxfreaker_at_gmail.com>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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