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From: Jason Swails <jason.swails.gmail.com>

Date: Mon, 12 Jan 2015 08:28:07 -0500

*> On Jan 12, 2015, at 5:12 AM, Houcemeddine Othman <houcemoo.gmail.com> wrote:
*

*>
*

*> Hi,
*

*> This is may be a generic question. I am trying to run free energy
*

*> decomposing on a protein-protein complex with 5500 (36 amino acids for the
*

*> ligand and 333 for the receptor) atoms. The simulation took nearly one week
*

*> and it is still running. I tried the Ras-Raf case complex from Amber
*

*> tutorials and it took just 3h to complete the simulation. I would like to
*

*> know if there is a way to estimate the calculation time required for the
*

*> calculation.
*

What calculation took nearly 1 week? The original MD calculation or the MM/GBSA calculation?

MM/GBSA should not take this long unless you are analyzing way too many frames. MM/PBSA calculations with decomposition might take a lot longer, depending on your settings (and normal mode calculations will take even longer still).

To estimate how long the MD simulation will take is easy -- the Amber output contains how many ns can be completed each day: divide the total simulation time you want by that metric and you get the number of days that the MD simulation will take.

To estimate how long the MM/GBSA calculation should take, analyze a subset of the frames (in your example input file, you are only analyzing 10 frames, which is good). If you have 200 frames in reality, then multiply the total time taken for 10 frames by 20 in order to get how long (approximately) it will take to finish 200 frames.

HTH,

Jason

*>
*

*>
*

*> input file:
*

*> &general
*

*> endframe=10, verbose=1,
*

*> /
*

*> &gb
*

*> igb=5, saltcon=0.150,
*

*> /
*

*> &decomp
*

*> idecomp=1,
*

*> dec_verbose=0,
*

*> print_res="334-369"
*

*> /
*

*>
*

*> Best regards
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

Date: Mon, 12 Jan 2015 08:28:07 -0500

What calculation took nearly 1 week? The original MD calculation or the MM/GBSA calculation?

MM/GBSA should not take this long unless you are analyzing way too many frames. MM/PBSA calculations with decomposition might take a lot longer, depending on your settings (and normal mode calculations will take even longer still).

To estimate how long the MD simulation will take is easy -- the Amber output contains how many ns can be completed each day: divide the total simulation time you want by that metric and you get the number of days that the MD simulation will take.

To estimate how long the MM/GBSA calculation should take, analyze a subset of the frames (in your example input file, you are only analyzing 10 frames, which is good). If you have 200 frames in reality, then multiply the total time taken for 10 frames by 20 in order to get how long (approximately) it will take to finish 200 frames.

HTH,

Jason

-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Jan 12 2015 - 05:30:05 PST

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