Dear Bill,
thanks for that clarification!
Best,
Anselm
On 02/20/2024 01:03 AM, Bill Miller III via AMBER wrote:
> Entropy=1 in the &general section calls for the quasi-harmonic method to be used.
>
> Putting the &nmode section in the MMPBSA input file calls for the normal mode entropy calculation to be used.
>
> So you are, in fact, specifying both to be used in your input file. If you only want to use one, then exclude the other in the MMPBSA input file.
>
> The calculation time for the quasi-harmonic is completely different from the normal mode calculation. It usually takes less time, but the resulting entropy is very dependent on the number of frames used for the calculation, and in general, I consider it less reliable for that reason.
>
> -Bill
>
>
>
>> On Feb 19, 2024, at 3:45 AM, Dr. Anselm Horn via AMBER <amber.ambermd.org> wrote:
>>
>> Dear Amber experts,
>>
>> I recently ran a test entropy calculation on a single frame of a MD
>> trajectory to obtain an nmode calculation result and an estimation of
>> the necessary computational resources; however, after the standard nmode
>> calculation, a second entropy calculation method (quasiharmonic), which
>> obtains the entropy from the trajectory analysis, seems to be triggered
>> automatically!
>>
>> In the Amber 23 manual (section 38.3.1) I could not find any clear
>> description of selecting the methods within the &nmode input section;
>> the MMPBSA.py introduction (section 38.1) just states that two entropy
>> calculation methods are available.
>>
>> How can I select either or both of the entropy calculation methods?
>>
>> (Can the computation time for the quasiharmonic analysis roughly be
>> guessed from the time necessary for a single nmode calculation?)
>>
>> I included the MMPBSA output (calculation still running) and my input
>> file at the end of this e-mail.
>>
>> Any help is appreciated!
>>
>> Best regards,
>>
>> Anselm
>>
>> Bioinformatik | NHR.FAU
>> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
>> Germany
>>
>>
>>
>> ------- STDOUT from the MMPBSA.py run
>>
>> Loading and checking parameter files for compatibility...
>> cpptraj found! Using /data1/soft/amber22at23/bin/cpptraj
>> mmpbsa_py_nabnmode found! Using
>> /data1/soft/amber22at23/bin/mmpbsa_py_nabnmode
>> Preparing trajectories for simulation...
>> 502 frames were processed by cpptraj for use in calculation.
>> 1 frames were processed by cpptraj for nmode calculations.
>>
>> Running calculations on normal system...
>>
>> Beginning nmode calculations with
>> /data1/soft/amber22at23/bin/mmpbsa_py_nabnmode
>> calculating complex contribution...
>> calculating receptor contribution...
>> calculating ligand contribution...
>>
>> Beginning quasi-harmonic calculations with
>> /data1/soft/amber22at23/bin/cpptraj
>>
>>
>> ------- Input file for the MMPBSA.py run
>>
>> # MMGBSA input / interaction energy
>> &general
>> verbose=2,
>> keep_files=1,
>> netcdf=1,
>> entropy=1,
>> /
>> &nmode
>> nmstartframe=1,
>> nmendframe=1,
>> nmode_igb=1,
>> nmode_istrng=0.0,
>> /
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 20 2024 - 03:00:02 PST
