AW: Link between simulations

From: Norman Geist (
Date: Wed Apr 24 2013 - 02:09:13 CDT



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 []
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?





On Mon, Apr 22, 2013 at 2:34 AM, Norman Geist
<> 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


And last but not least, there's a very nice NAMD manual and tutorial out


Norman Geist.


Von: [] Im Auftrag
von Mihaela Drenscko
Gesendet: Samstag, 20. April 2013 22:19
Betreff: namd-l: Link between simulations




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


Thank you,




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