From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Wed Apr 24 2013 - 04:30:12 CDT
Dear Mihaela,
You are right, Norman shouldn't answer you at all. Actually I am surprise
that he did. The things you ask are the basics one should now before start
using NAMD and you would know the answers to your questions if you have
spent some time searching in google, in the mailing list or in the
documentation. Let me give you a little help with that:
http://lmgtfy.com/?q=pbs+jobs+dependencies
http://lmgtfy.com/?q=namd+how+to+use+restart+files
On 24 April 2013 10:09, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:
> Mihaela,****
>
> ** **
>
> If someone asks how to combine two trajectories of the same simulation,
> that would have been a normal question. If someone asks how to combine
> trajectories in addition with how to use restart files, this sound like
> cheating together two different simulations, that have not been staged on
> each other, to one and such kind of questions earns such kind of answers.
> Additionally many questions could easily be solved by simply reading the
> manual, btw. like your question, too. Some people seem to think, that a
> mailing list is supposed to support people that are too lazy to inform
> themselves, so please don’t wonder when people are annoyed sometimes and be
> happy to get an answer at all, OK?****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* Mihaela Drenscko [mailto:quo.physics_at_gmail.com]
> *Gesendet:* Dienstag, 23. April 2013 18:31
> *An:* Norman Geist
> *Betreff:* Re: namd-l: Link between simulations****
>
> ** **
>
> Thank you, Norman.****
>
> ****
>
> On the other hand, if you are going to use words such as "nonsense" and
> "abuse", better don't answer at all, OK?****
>
> ****
>
> Mihaela****
>
> ****
>
> ** **
>
> On Mon, Apr 22, 2013 at 2:34 AM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:****
>
> Hi Mihaela,****
>
> ****
>
> this is nonsense and abuse all people that do serous theoretical research
> by molecular dynamics. Firstly, because you cannot link together two
> trajectories that molecules has gone two different
> timelines(ways/realities). Secondly because running 10 ns is running 10 ns,
> no matter if two times 5 or 10 in a bunch, it will take the same time.****
>
> ****
>
> What you need to do, is to restart from the point, where your job has been
> killed. Btw it’s not unusual that on high performance computing centers,
> the jobs get killed every 24 hour or similar, to provide time windows for
> maintenance and to kill jobs that are not watched by the owner and so are
> like “dead bodies” that occupy resources. To restart you simulation, you
> will have to modify the input to use the latest coordinates, velocities and
> cell dimensions.****
>
> ****
>
> Therefore change coordinates that it uses the “restart.coor” file and add
> velocities to your “restart.vel” and extendedsystem to “restart.xsc” and
> remove “temperature” as you already have your temperature due the
> velocities.****
>
> ****
>
> And last but not least, there’s a very nice NAMD manual and tutorial out
> there.****
>
> ****
>
> Norman Geist.****
>
> ****
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Mihaela Drenscko
> *Gesendet:* Samstag, 20. April 2013 22:19
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* namd-l: Link between simulations****
>
> ****
>
> Hi,****
>
> ****
>
> I was running a simulation with 10 million steps for DMPC molecule. The
> job was killed by high performance computing because it took too much time.
> So I decided to divide the job in two parts, each with 5 million steps.
> Now, how do I link the second job with the first, so that in the end it
> will look like I have run the simulation with 10 million steps? How do I
> use restart files?****
>
> ****
>
> Thank you,****
>
> ****
>
> Mihaela****
>
> ** **
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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