From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Tue May 14 2013 - 00:02:34 CDT
The NAMD tutorial is helpful:
See for example, "Ubiquitin in a Water Box". It provides sample files how
to run it.
On Mon, 13 May 2013, Aron Broom wrote:
> I think you may need to read a bit more about what NAMD does, how it runs and what its
> inputs are. But the short answer to your question is no, you can't just supply the
> coordinates. The user manual and tutorials on the main site are particularly good sources
> of information.
> As has already been mentioned there already exist benchmarking systems that you can use
> which cover a range of sizes, and which would allow you to compare against other hardware.
> These are ready to use so would save some time.
> Have you opened the src/alanin file that you ran to see what the input was? Moreover, how
> do you even know the run completed successfully? The 0.0085 seconds could be the time it
> took to fail from an inappropriate input.
> On Mon, May 13, 2013 at 10:02 PM, linux freaker <linuxfreaker_at_gmail.com> wrote:
> 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 <rswett_at_chem.wayne.edu> 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
> The acronym PDB stands for protein data bank, www.pdb.org is the
> repository of known crystal structures. Used as a file extension, it
> crystallographic coordinates saved in the standardized protein data bank
> format. www.pdb.org 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 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>
> 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 Ljubeti?"
> <ajasja.ljubetic_at_gmail.com> wrote:
> Here is a ready to run benchmark (apo1)
> http://www.ks.uiuc.edu/Research/namd/performance.html (Direct
> On 13 May 2013 18:52, Cesar Millan <pachequin_at_gmail.com>
> 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
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
+1 (206) 685 4435
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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