Thread: [apbs-users] Post-processing of MD trajectories
Biomolecular electrostatics software
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From: Davide M. <dm...@au...> - 2012-07-04 01:19:37
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Dear All, I have performed a series of electrostatic calculations on MD trajectories for a macromolecular complex using APBS, and I have recorded at each time step (every 10 ps for a total simulated time of 50 ns) the electrostatic binding energy for the complex formation, obtained by subtracting the electrostatic binding energies of the single binding partners from the electrostatic binding energy of the complex. With the help of a little script I have then plotted the electrostatic binding energy as a function of the simulated time. Overall, I get a nice profile that corresponds to what I expected. However, along the simulated time the graph is spiky. At some time steps the energy drops suddenly down (I would expect a little spike but not a variations of a couple of orders of magnitude). Can you please help me to understand why this happens? Can this be due to the fact that the change in conformation of the ligand and/or target has as an effect the neutralization of some charges and causes the drop of the electrostatic binding energy? It is physically possible or it's an artifact? I wanted to attach the obtained graph and .pqr files to the e-mail but I had no luck with it as the attachments get rejected. If you need to see the files can you please let me know how I can attach them? The attachments are not bigger than few KB altogether. I have been using a "focusing" approach to calculate the electrostatic binding energy. Any help will be greatly appreciated. Thank you very very much in advance. Davide Mercadante |
From: Baker, N. <Nat...@pn...> - 2012-07-04 23:33:50
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Hi Davide - Are you using the same grid spacing and position for all calculations? Variations in the grid setup could cause big changes in energy. Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me<http://nabaker.me/> From: Davide Mercadante [mailto:dm...@au...] Sent: Tuesday, July 03, 2012 5:41 PM To: apb...@li... Subject: [apbs-users] Post-processing of MD trajectories Dear All, I have performed a series of electrostatic calculations on MD trajectories for a macromolecular complex using APBS, and I have recorded at each time step (every 10 ps for a total simulated time of 50 ns) the electrostatic binding energy for the complex formation, obtained by subtracting the electrostatic binding energies of the single binding partners from the electrostatic binding energy of the complex. With the help of a little script I have then plotted the electrostatic binding energy as a function of the simulated time. Overall, I get a nice profile that corresponds to what I expected. However, along the simulated time the graph is spiky. At some time steps the energy drops suddenly down (I would expect a little spike but not a variations of a couple of orders of magnitude). Can you please help me to understand why this happens? Can this be due to the fact that the change in conformation of the ligand and/or target has as an effect the neutralization of some charges and causes the drop of the electrostatic binding energy? It is physically possible or it's an artifact? I wanted to attach the obtained graph and .pqr files to the e-mail but I had no luck with it as the attachments get rejected. If you need to see the files can you please let me know how I can attach them? The attachments are not bigger than few KB altogether. I have been using a "focusing" approach to calculate the electrostatic binding energy. Any help will be greatly appreciated. Thank you very very much in advance. Davide Mercadante |
From: Davide M. <dm...@au...> - 2012-07-04 23:41:38
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Dear Nathan, Thanks for your reply. Yes..all the parameters are exactly the same.. Thank you Davide Davide Mercadante PhD student - School of Chemical Sciences The University of Auckland New Zealand On 5/07/2012, at 11:33 AM, "Baker, Nathan" <Nat...@pn...> wrote: > Hi Davide – > > Are you using the same grid spacing and position for all calculations? Variations in the grid setup could cause big changes in energy. > > Thanks, > > __________________________________________________ > Nathan Baker > Pacific Northwest National Laboratory > Tel: +1-509-375-3997 > http://nabaker.me > > From: Davide Mercadante [mailto:dm...@au...] > Sent: Tuesday, July 03, 2012 5:41 PM > To: apb...@li... > Subject: [apbs-users] Post-processing of MD trajectories > > Dear All, > > I have performed a series of electrostatic calculations on MD trajectories > for a macromolecular complex using APBS, and I have recorded at each time > step (every 10 ps for a total simulated time of 50 ns) the electrostatic > binding energy for the complex formation, obtained by subtracting the > electrostatic binding energies of the single binding partners from the > electrostatic binding energy of the complex. > > With the help of a little script I have then plotted the electrostatic > binding energy as a function of the simulated time. > > Overall, I get a nice profile that corresponds to what I expected. However, > along the simulated time the graph is spiky. At some time steps the energy > drops suddenly down (I would expect a little spike but not a variations of a > couple of orders of magnitude). Can you please help me to understand why > this happens? Can this be due to the fact that the change in conformation of > the ligand and/or target has as an effect the neutralization of some charges > and causes the drop of the electrostatic binding energy? It is physically > possible or it's an artifact? > > I wanted to attach the obtained graph and .pqr files to the e-mail but I had no luck with it as the attachments get rejected. > If you need to see the files can you please let me know how I can attach them? > The attachments are not bigger than few KB altogether. > > I have been using a "focusing" approach to calculate the > electrostatic binding energy. > > Any help will be greatly appreciated. > > Thank you very very much in advance. > > Davide Mercadante |