Thank you very much for all your help.
I will try to avoid the transition from Amber 14 to Amber 16.
I hope I can use ntt=5 and nchain=4 also in Amber 14 (in order to activate Nosé-Hoover thermostat).
Thanks again
Giovanna
________________________________
Da: David A Case <david.case.rutgers.edu>
Inviato: mercoledì 8 agosto 2018 15:41
A: AMBER Mailing List
Oggetto: Re: [AMBER] problem with amber 16
On Wed, Aug 08, 2018, giovanna rogati wrote:
>
> I am a beginner user (dummy actually!!!) of AMBER, I create a input for
> minimization that runs on amber 14. Now I would like to use amber 16 (I
> would like to add Nosé Hoover thermostat in run production). I have the
> same topology file, the same initial coordinates and box size, the same
> input... and I launch sander. The simulation run, but sander, in AMBER
> 14 write output coordinates, instead in AMBER 16 does not write the
> output coordinates (this produces only a unreadable file of coordinates
> equal to that of restart).
The default format for restart files changed at the Amber14 -> Amber16
update. It's always difficult to upset backwards compatibility, and we
in general try to avoid that. But the benefits of the binary format are
so great that we decided to push users in that direction. You can set
the "ntxo" variable to a non-default value if you want/need the old
behavior.
That said, I'm not sure I understand your question: "produces an
unreadable file of coordinates equal to that of the restart". Exactly
which file is unreadable? The format of the trajectory file (created
with the -x flag) is controlled by ioutfm.
>
> I try with cpptraj but produce only atoms coordinates at the last step
> of simulation... I would like a trajectory
> cpptraj -p ${TOP} -y Stac_md$A.rst -x Stac_md$A.pdb
> cpptraj -p ${TOP} -y Stac_md$A.rst -x prova.crd
Assuming that the above commands are what you tried: try running cpptraj
interactivly, using the "parm", "trajin" and "trajout" commands to
specify the conversions you want. cpptraj may give more helpful
messages about what it is doing in that case. cpptraj should
auto-detect the restart file format, but you may need to tell it
explicitly the output format you want.
Finally, the above cpptraj commands read in the restart file, so of
course you will only get an output that has coordinates for the final
step.
...hope this helps....dac
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Received on Wed Aug 15 2018 - 23:30:02 PDT
