Re: [AMBER] Problem related to the umbrella sampling

From: Sindrila Dutta banik <>
Date: Fri, 12 Jul 2013 12:23:22 +0800 (SGT)

Thanks once again.á One article is attached (JACS, 2006, 128, 16345) where they compute PMF classically and compare it with QM. Can I do similar study using Amber, if yes then how?á I initially thought that I can do similar study using umbrella sampling using two constrains as I described in my previous mail. Is this correct?á With regards Sindrilaá ________________________________ From: Jason Swails <> To: Sindrila Dutta banik <> Sent: Friday, 12 July 2013 12:11 AM Subject: Re: [AMBER] Problem related to the umbrella sampling On Thu, Jul 11, 2013 at 2:27 PM, Sindrila Dutta banik <> wrote: Thanks for your kind reply.á > > >Yes, these two bonds involve in the proton transfer reaction. á > > >As you told in your previous mail: "You cannot make or break bonds using a force field" I also agree with this. >But I could not understand how people calculate PMF for proton transfer process using classical mechanics using umbrella sampling. There are many papers where people calculate energy barrier using classical mechanics as well as QM and compare the barrier height.á Are you sure they don't use QM/MM? áYou can use a Morse potential to model a breakable bond within the context of a classical force field, but I have not read of any studies that use this approach. áQM/MM approaches, on the other hand (in which the reactive center is in the QM region, obviously) are abundant. Deforming heavy atom-hydrogen bonds in a classical force field (or any bond, really), is a recipe for disaster. áBonds are assumed to be harmonic---an approach that is only valid when the bond is close to its equilibrium value (the same is true of force fields that employ a quartic term, although they are accurate at slightly larger deviations). > >Iálook at atomsá10018 and 10019 in my system. But every thing is fine with this atoms. But the substrate (PPD for which noshake is applied) is deformed during this run. And the above mentioned atoms are not the part of substrate. Is the increase in bond length from 1.1A to 1.7A is too large? Is the problem arises due to large increment in separation?á The bond strengths are likely very large (~300-400 kcal/mol/┼^2), so these deviations are causing a huge force to be put on your system. áIt's pretty easy to see how this can destroy a simulation (it appears that 1.7 ┼ is the tipping point). Also, if you see a SHAKE error involving an atom that appears to be part of the noshakemask selection, it is worth checking your mask to make sure that it is selecting the atoms you want it to select (the ambmask program helps with this). Good luck, Jason -- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032

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Received on Thu Jul 11 2013 - 21:30:05 PDT
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