Dear Case,<br/><br/> Firstly, for a standard simulation with QM/MM Hamiltonian, it can terminate correctly.<br/><br/> Then, for the TI simulation, when the build-in semi-empirical PM3 method replace the external B3LYP method, the calculation can also terminate correctly.<br/><br/> For the TI calculation by sander.MPI, two groups will run in parallel. However, they use the files with the same name "extern_location" in the same directory. Maybe it is this reason that causes the error.
At 2016-06-27 20:07:18, "David A Case" <david.case.rutgers.edu> wrote:
>On Mon, Jun 27, 2016, Xiangyu Jia wrote:
>>
>> Recently, Thermodynamic Integration method was used to calculate
>> the free energy difference between two states in my research.
>> Particularly, the Hamiltonians of both states were described by
>> QM/MM. However, the calculation stopped with the following error
>> message:
>>
>> "SANDER BOMB in subroutine check_installation
>> (qm2_extern_util_module). Internal error closing and deleting files with
>> path location of executable. Quitting now."
>>
>> So, does Sander.MPI support TI calculation for both states described
>> by QM/MM Hamiltonian ? Otherwise, how can I fix this problem ?
>
>Just to help the debugging:
>
>1. Can you confirm that a standard (non-TI) calculation, with everything else
>the same, runs OK?
>
>2. Please try a short TI run using one of the built-in QM Hamiltonians, such
>as PM6. Does this trigger any errors?
>
>...dac
>
>
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Received on Mon Jun 27 2016 - 07:30:02 PDT
