Dear Jason,
Thank you a lot for your answer!
I’ll do so.
Ruth
> On 02 Nov 2015, at 15:17, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Mon, Nov 2, 2015 at 9:13 AM, Ruth Helena Tichauer <rhtichau.laas.fr <mailto: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 - 06:30:05 PST
