On Mon, Nov 2, 2015 at 9:13 AM, Ruth Helena Tichauer <rhtichau.laas.fr>
wrote:
> Dear David,
>
> Thank you a lot for the answer!
>
> I’m running sander with the following command:
>
> $AMBERHOME/exe/sander -i density.in -p ala.asmd.prmtop -c ala.asmd_ht.rst
> -ref ala.asmd_ht.rst -o ala.asmd_den.out -r ala.asmd_den.rst -x
> ala.asmd_den.nc &
>
> When typing the command “$AMBERHOME/update_amber —version” I have no
> answer (I guess update_amber is not in that directory) but I think that
> amber 11 is the version installed in the computer I use as “$AMBERHOME"
> stands for "/opt/amber11-gnu/."
>
Amber 11 is a very old version of Amber (from ~2010) that pre-dates
update_amber as well as the barostat keyword. I would recommend updating
to AmberTools 15, which you can install in your home directory without root
privileges and which includes sander.
> I tried again to run the density equilibration step of tutorial A26, first
> with barostat=1 in the input file which lead to the same error message,
> then, I removed this functionality, and it worked (or at least the MD
> production is running for now). Is it “useful” to do the density
> equilibration step of the system if the pressure regulation isn’t available
> in the amber version I use?
>
The 'barostat' keyword was introduced as a way to select between the
Berendsen barostat and the newly-implemented Monte Carlo barostat. In
versions before Amber 14, the only available barostat was Berendsen, and
the "barostat" keyword did not exist.
So as long as you set ntp=1 and ntb=2 in your input file, the system will
equilibrate its density, even if the barostat keyword isn't supported.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 02 2015 - 06:30:04 PST
