Dear all, I solved the problem modifying the source file
amoeba_direct.F90, when the variables are defined, turning the default
1.025 into 10.25. Maybe ten times is too much..but the simulations run
well in my case.
You can try something similar
_REAL_,parameter :: safety = 10.25d0, checklist = 0.9d0
Bye
Lorenzo
On 29/10/14 12:38, David A Case wrote:
> On Wed, Oct 29, 2014, Ya Gao wrote:
>> I performed a MD simulation under amoeba force field with pmemd.amoeba.MPI
>> in amber14.
>>
>> The minimization terminates normally. However, when the heat simulation
>> reached 9.0 ps, it was interrupted with the message " Too many
>> dipole_dipole interactions for allocated".
> I haven't seen this in a long time. How big is your system? What is the
> value of size_dipole_dipole_list (printed in the mdout file)? It seems quite
> odd that your temperature is still less than 2 K after 9 ps of simulation.
> Have you run other systems with amoeba?
>
> Since you have a trajectory with snapshots every 500 steps, I'd suggest first
> looking at that to see what is going on. A second step is to run a
> simulation with the serial version of pmemd.amoeba, to see if this might have
> something to do with the MPI code.
>
> Another thing to do is to Google "amber Too many dipole_dipole
> interactions for allocated", and try increasing the "safety" parameter as
> described there.
>
> If those steps don't help, you will probably have to post files that would
> allow someone else to reproduce the problem.
>
> ...regards...dac
>
>
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--
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Lorenzo Gontrani
Research associate - EDXD group
University of Rome "La Sapienza"
GSM +39 338 7615798
Email lorenzo DOT gontrani AT gmail DOT com
Webpage: http://webcaminiti/gontrani.html
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Received on Wed Oct 29 2014 - 05:00:03 PDT
