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/."
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?
Thanks again for your time,
Ruth
P.S. Input file:
Density Equilibration
&cntrl
imin=0, nstlim=250000, dt=0.002,
irest=1, ntx=5,
ntc=2, ntf=2, ntb=2, ntp=1, taup=1.0,
cut=8.0, iwrap=1, ig=-1,
ntpr=10000, ntwx=10000, ntwr=10000,
ntt=3, gamma_ln=5.0, temp0=300.0,
ntr=1, restraintmask=':1-12', restraint_wt=20.0,
ioutfm=1,
/
> On 02 Nov 2015, at 13:37, David A Case <david.case.rutgers.edu> wrote:
>
> On Mon, Nov 02, 2015, Ruth Helena Tichauer wrote:
>>
>> error in reading namelist cntrl
>
> Unfortunately, many Fortran compilers fail to give detailed information about
> namelist errors. You have to use trial and error, eliminating variables until
> things "work", then adding the discarded ones back in slowly.
>
> My guess(!) is that your version of Amber doesn't support the "barostat"
> variable, since this is a relatively recent addition. If this doesn't help,
> let us know that program you are running, and which version of Amber you have.
>
> ....dac
>
>
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Received on Mon Nov 02 2015 - 06:30:03 PST
