[gmx-users] Problems for restarting a job after 10ns run

Yuhua Song yhsong at ccb.wustl.edu
Mon Mar 15 22:05:01 CET 2004

My case is that I save every 2ps for coordinates, every 100ps for velocity.
so for total 10ns, I assume totally have 5000+1 frames. The key is the
frequency that I save coordinate and velocity are not same, so the size of
every frame should be not equal, right? Now, I met the situation, after I
split the frame in the same size, when I use tpbconv, it shows the error for
reading the splitted *.trr file.

Someone had met this situation, and can give me some inputs?



----- Original Message ----- 
From: <tamara-frembgenkesner at uiowa.edu>
To: <gmx-users at gromacs.org>
Sent: Monday, March 15, 2004 11:23 AM
Subject: Re: [gmx-users] Problems for restarting a job after 10ns run

> Try using the split command, with -b to specify file size:
> split -b (filesize) *.trr junk
> Use the last junk file (they will be labelled junkaa, junkab, etc.) to
> with.
> Tam
> Quoting Yuhua Song <yhsong at ccb.wustl.edu>:
> > Dear Gromacs Colleagues:
> >
> > After 10 ns run, I got a 3.2 G  *.trr file, I want to restart the run
> > another 10ns, I met the following problems:
> >
> > 1) if I use "tpbconv" , it needs to read the full precision trajectory
> > but the generated *.trr file is too large, the system can not recognize
> > file. Although I write out the *.xtc file, but *.xtc file has only the
> > coordinate info, not velocity info, seems not proper for the input file
> > "tpbconv" for the restart purpose
> >
> > 2) if I use "grompp",  there is the -c option, it read in the Generic
> > structure. My quesiton is although when I write *.gro file, I write out
> > the coordinate and velocity info, so when using -c option to read the
> > it will also read into the velocity info? For the restart purpose, I
> > need to use "-t " option to read into the starting coordinate and
> > info for restart purpose, right?
> >
> > 3) With "grompp", the manual said: starting coodinates can be read from
> > trajectory with "-t" option, but it need to read the " *.trr" file. This
> > again meet the large *.trr file issue.
> >
> > So, I am wondering someone can give me some suggestion about how to
> > the restart issue after 10ns or longer runs?
> >
> > Thank you very much,
> >
> > Yuhua
> >
> >
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