Re: is the aMD implementation compatible with AMBER force fields

From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Wed Jun 18 2014 - 18:20:00 CDT

Thank you Jeff!

I want to ask you something irrelevant to the topic: is it correct to
combine two simulations with different (but close) boost values and
reweight them to derive the equilibrium distribution of conformational
states in the usual way (histogram)? I basically ran a few hundreds of
nanoseconds and then continued using a lower boost.

thanks,
Thomas

On 18 June 2014 21:14, Jeff Wereszczynski <jwereszc_at_iit.edu> wrote:

> Hi Thomas,
>
> Yes, in theory you can still go ahead and use these for reweighing if the
> aMD code isn't taking into account the LJCorrection energy. Its analogous
> to only boosting the dihedrals and not the total potential energy.
>
> Cheers,
> Jeff
>
> Jeff Wereszczynski
> Assistant Professor of Physics
> Illinois Institute of Technology
> http://www.iit.edu/~jwereszc
>
>
> On Wed, Jun 18, 2014 at 6:20 AM, Thomas Evangelidis <tevang3_at_gmail.com>
> wrote:
>
>> Greetings,
>>
>> My query is a possible problem of the aMD implementation in NAMD 2.10
>> (CVS-2013-11-09) in the case of explicit solvent simulation with the AMBER
>> ff. In the 2011 paper about the aMD implementation, CHARMM ff was used.
>> However, in order to use an AMBER ff in NAMD I have to switch on the
>> LJcorrection. In that case the vdW and Potential energies printed in the
>> "ACCELERATED MD:" line are different from those in the "ENERGY:" line. In
>> contrast, when I switch off the LJcorrection flag all the energies are
>> identical. Have a look at some sample lines:
>>
>>
>> with LJcorrection on:
>>
>> ACCELERATED MD: STEP 87543000 dV 72.2669 dVAVG 82.8525 BOND 5288.23 ANGLE
>> 18672.4 DIHED 16735.6 IMPRP 0 ELECT -204303 VDW 15665.3 POTENTIAL -147940
>> ETITLE: TS BOND ANGLE DIHED
>> IMPRP ELECT VDW BOUNDARY MISC
>> KINETIC TOTAL TEMP POTENTIAL
>> TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME
>> PRESSAVG GPRESSAVG
>> ENERGY: 87543000 5288.2277 18672.4165 16735.6300
>> 0.0000 -204302.7087 13520.8743 0.0000 1.6135
>> 47684.6230 -102399.3237 311.5958 -150083.9467
>> -102080.5748 311.3023 -259.4794 -246.9799
>> 738674.3246 -29.1724 -29.0266
>>
>> with LJcorrection off:
>>
>> ACCELERATED MD: STEP 87543000 dV 76.7961 dVAVG 94.015 BOND 5120.57 ANGLE
>> 18918.2 DIHED 16759.4 IMPRP 0 ELECT -204135 VDW 15280.7 POTENTIAL -148058
>> ETITLE: TS BOND ANGLE DIHED
>> IMPRP ELECT VDW BOUNDARY MISC
>> KINETIC TOTAL TEMP POTENTIAL
>> TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME
>> PRESSAVG GPRESSAVG
>> ENERGY: 87543000 5120.5713 18918.1941 16759.3518
>> 0.0000 -204135.4881 15280.7398 0.0000 -1.3280
>> 47291.1523 -100766.8069 309.0247 -148057.9592
>> -100448.3863 309.6632 -155.2256 -154.3696
>> 726366.2601 -22.7045 -22.6922
>>
>>
>> Apparently the analytical tail correction is not considered in dV
>> calculation, which results to a moderate overestimation of the potential
>> energy and consequently to a lower boost, which is not bad. Do you reckon I
>> can still use these dV values for reweighting? I don't see any problem
>> using them, just wanted to have the expert opinion of a more experienced
>> user/developer.
>>
>>
>> thanks in advance,
>> Thomas
>>
>>
>>
>

-- 
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
          tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/

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