[gmx-users] problem implementing REST2 in GROMACS 4.6.5

[Elio Fiorentini]

Hi, Mark.
Thanks a lot for your kind reply. I am filing the issue on the website you
mentioned. Please let me know at your earliest convenience whether the
problem can be sorted out or it is better to resort to a previous gromacs
version in the meanwhile (it seems that REST2 can be implemented easily on
4.5.5, although I have not tried that, since it is not installed on our
cluster), so as to get some results on this system in a reasonable time.
Thanks a lot for your help!
Elio

2015-09-16 10:55 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> That does look like a code problem, but I can't imagine how. Can you please
> open an issue at http://redmine.gromacs.org, and upload .tpr and .log
> files
> so we can see what is going on?
>
> Thanks!
>
> Mark
>
> On Mon, Sep 14, 2015 at 1:22 PM Elio Fiorentini <
> elio.fiorentini90 at gmail.com>
> wrote:
>
> > I report an example :
> >
> > file md0.log
> > Step           Time             Lambda
> >  200       2000.20000        0.00000
> >
> >    Potential              Total Energy
> >    -3.15120e+05      -2.53064e+05
> >
> > Replica exchange at step 200 time 2000.2
> > Repl 0 <-> 1  dE_term =  0.000e+00 (kT)
> > Repl ex  0 x  1    2 x  3    4 x  5    6 x  7    8 x  9   10 x 11
> > Repl pr   1.0       1.0       1.0       1.0       1.0       1.0
> >
> >
> >
> -------------------------------------------------------------------------------------------
> >
> > file md1.log
> > Step           Time             Lambda
> >  200       2000.20000        0.14100
> >
> >    Potential              Total Energy
> >    -3.15895e+05      -2.53743e+05
> >
> > Replica exchange at step 200 time 2000.2
> > Repl 0 <-> 1  dE_term =  0.000e+00 (kT)
> > Repl ex  0 x  1    2 x  3    4 x  5    6 x  7    8 x  9   10 x 11
> > Repl pr   1.0       1.0       1.0       1.0       1.0       1.0
> >
> >
> >
> --------------------------------------------------------------------------------------------------------------------
> >
> > file md2.log
> > Step           Time             Lambda
> >  200       2000.20000        0.26840
> >
> >    Potential              Total Energy
> >    -3.16544e+05      -2.54358e+05
> >
> > Replica exchange at step 200 time 2000.2
> > Repl 2 <-> 3  dE_term =  0.000e+00 (kT)
> > Repl ex  0 x  1    2 x  3    4 x  5    6 x  7    8 x  9   10 x 11
> > Repl pr   1.0       1.0       1.0       1.0       1.0       1.0
> >
> >
> >
> --------------------------------------------------------------------------------------------------------------------------
> >
> > file md3.log
> > Step           Time             Lambda
> >  200       2000.20000        0.3836
> >
> >    Potential              Total Energy
> >    -3.17757e+05      -2.55540e+05
> >
> > Replica exchange at step 200 time 2000.2
> > Repl 2 <-> 3  dE_term =  0.000e+00 (kT)
> > Repl ex  0 x  1    2 x  3    4 x  5    6 x  7    8 x  9   10 x 11
> > Repl pr   1.0       1.0       1.0       1.0       1.0       1.0
> >
> >
> >
> -------------------------------------------------------------------------------------------------------------------------------------------
> >
> > and so on
> > --
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