Re: [AMBER] problems in nmode and -use-mdins option (

From: houcemeddine <>
Date: Tue, 24 Dec 2013 20:09:15 +0100

Hi Jason,
Thank you for the reply. Sorry for not mentioning that the input file
posted before was only used for rapid testing mainly to evaluate the
computation time. I actually used maxcyc=10000. The calculation run now
for 2 days and still not completed. I guess I have to check if I could
neglect the entropy term for my system.

best regards

On 12/24/2013 07:31 PM, Jason Swails wrote:
> On Tue, Dec 24, 2013 at 10:55 AM, houcemeddine <> wrote:
>> Hi everybody,
>> I run some tests for to estimate the free energy using GB, and
>> Nmode for a protein-protein complex (nearly 5500 atom) in order to rank
>> some docking poses.
>> Using maxcyc=10 and 20 runs the calculation simultaniously for 15 and
>> 30 min for only one snapshot.
> maxcyc=10 or 20 is WAY too low unless the trajectory has already been
> minimized. It typically takes thousands of minimization steps for the
> structures to minimize within allowable tolerances for the normal mode
> calculation. When you set maxcyc=10 or 20, the structure will minimize,
> realize it is not minimized enough, then quit without calculating the
> normal modes (or at least that's what it should do). You should keep
> maxcyc large, and the minimization will stop once the gradient falls below
> a certain threshold (drms).
>> I am aware that the entropy term is
>> computationaly expensive, however in my case it seems that the
>> calculation converges very slowly while my estimations of computation
>> time is 10 days/snapshot
> This is not unusual, and is the primary reason normal mode calculations are
> often avoided when possible. The minimization procedure can take a very
> long time, as can the hessian construction (and diagonlization) itself.
> For very large systems, 10 days may be fairly typical.
> Does someone have any idea about this issue?
>> I also desired to use an input file to tune the parameters for Nmode
>> with -use-mdins flag. The issue is that only the _MMPBSA_gb.mdin is
>> generated at the end of the calculation but not
>> _MMPBSA_sander_nm_min.mdin neither were present even if
>> I use the -make-mdins flag. is there any explanation for this ?
> Many calculations in are now done with pipes and command-line
> input rather than with temporary input files. Normal mode calculations are
> done by passing the necessary parameters to mmpbsa_py_nabnmode via the
> command-line, so no input file is ever created. This is not really much of
> a limitation, though, as all of the available options are accessible
> through the input file (unlike several options for GB and PB
> calculations).
> HTH,
> Jason

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Received on Tue Dec 24 2013 - 11:30:02 PST
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