[gmx-users] TRR file with nstxout= 0

[Mark Abraham]

On 30/04/2012 6:34 PM, Steven Neumann wrote:
>
>
> On Fri, Apr 27, 2012 at 5:13 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     On 4/27/12 12:09 PM, Steven Neumann wrote:
>
>
>
>         On Fri, Apr 27, 2012 at 4:38 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
>            On 4/27/12 11:34 AM, Steven Neumann wrote:
>
>
>
>                On Fri, Apr 27, 2012 at 4:28 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>> wrote:
>
>
>
>                    On 4/27/12 11:22 AM, Steven Neumann wrote:
>
>                        Dear Gmx Users,
>
>                        I am running 2 us simulation in implicit
>         solvent model:
>
>                        define        = -DPOSRES
>                        integrator    = sd        ; leap-frog integrator
>                        nsteps        = 500000000     ; 0.004 *
>         500000000= 2 us
>                        dt        = 0.004         ; 4 fs
>                        ; Output control
>                        nstxout       = 0
>                        nstxtcout    = 50000        ; xtc compressed
>         trajectory output
>                every 2 ps
>                        nstenergy    = 10000      ; save energies every
>         2 ps
>                        nstlog        = 10000     ; update log file
>         every 2 ps
>
>                        How come my trajectory (trr) is being created
>         and takes 80 GB?
>
>
>                    The default for nstvout is 100, so you're likely
>         getting very frequent
>                    output of velocities into the .trr file.
>
>                    -Justin
>
>                Thank you
>                This job crashed due to the quota exceeded. If change
>         my mdp file (with
>                additional nstvout=0)  using tpbconv and run it from
>         the checkpoint file it
>                should work then with no trr file?
>
>
>            If you need to change the .mdp file, you can't use tpbconv;
>         use grompp to
>            generate a new .tpr file and submit the new job.
>
>
>         So if I will create new mdp file (with additional nstvout=0 to
>         get rid of trr
>         files) and use:
>
>         mdrun -s new.tpr -cpi last.cpt
>
>         Will I continue from the checkpoint?
>
>
>     That's the question I posed below...
>
>
>              I'm not sure if you can pick up using mdrun -cpi if the
>         settings have
>            changed, but you can try.
>
>
>         Yes you can, from 4.0 you do not have to specify -append just
>         -cpi file if the
>         job crashed.
>
>
>     I am aware of checkpointing, but what I'm not sure of is if you
>     change output options (or others) mid-stream, if the checkpointing
>     mechanism will complain, particularly due to the changes in the
>     .trr content.  You'll have to try and see.
>
>
>     -Justin
>
> Indeed, it complains in terms of not present trr file (3 out of 4 
> files present) and he does not want to carry on. But when I change 
> name of the output it starts from the checkpoint  generating new files.

Yes, that will be the effect of the (default) mdrun -append yes in 4.5

> Can I then somehow connect those two xtc trajectories using trjconv?

Yes, or better trjcat. Be sure to read and understand their -h output first.

> Which tpr file I should use?

You don't even need a .tpr file to concatenate trajectory files.

Mark
> Steven
>
>
>     -- 
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120430/0ed13c1c/attachment.html>