[gmx-developers] tpic energies - COUL_SR
João M. Damas
jmdamas at itqb.unl.pt
Thu Mar 6 07:31:26 CET 2014
This interests me and I'd like to help you, but I'm currently swamped.
I cannot promise it, but I'll try to look at this.
On Fri, Feb 21, 2014 at 12:28 PM, Rui Fartaria <rui.fartaria at gmail.com>wrote:
> Hi all,
> I am a new user/developer of GROMACS. I am using GROMACS 4.6.3
> My goal is to extend the package GromPy, created by René Pool but I am
> still new to the code.
> In the meanwhile I wanted to calculate the excess chemical potential using
> TPI/TPIC. TPIC is preferable as my systems tend to be highly anisotropic
> and therefore TPIC allows me to choose where to sample.
> I noticed that some energies for the insertion of molecules were extremely
> low. To check if everything was working ok, I prepared the following test:
> - I have a configuration without the inserted molecule and the same
> configuration with the molecule inserted.
> - The molecule in question is monoethanolamine (MEA).
> - MEA topology was modified with nrexcl=5 so that intra molecular
> interactions were not an issue for comparing insertion energies.
> - I run 1 time step in each and then run "echo '1 2 3 4 5 6 0' |
> g_energy" to get the different terms for potential energy.
> - When calculating the differences between the "inserted" and "non
> inserted" configurations I corrected for the potential energy due to angles
> and dihedrals.
> - I hacked the tpi.c source code and forced it to insert the same
> configuration as in the tests described above.
> I prepared at tgz with the tests and the code for the hacked tpi.c. I can
> be downloaded from:
> As I have tested it, if you compile GROMACS 4.6.3 with the my modified
> version of tpi.c and run "bash run_examples.bash" in the example folder you
> should get the file result.txt as shown below (really hope it works for you
> You can see from the results below that the energies between the standard
> calculation for potential energy and the TPIC potential energy do not
> match. I searched the archives and the only reference to a problem like
> this was due to problems in the reciprocal sum in PME. In my case the
> problem is in the Coulomb real space sum. This is affected by a cutoff and
> I could not locate the exact place in the code where these calculations are
> The LJ sums match, apart from long range corrections. I also find it
> strange that the reciprocal part of the coulomb term is 0.0 in TPIC.
> I would be really thankful if someone could help me understand where the
> problem is. Hopefully you already know.
> Kind regards,
> Rui Fartaria
> Angle RB LJ Coul(SR) Coul(RECIP) Potential
> 15611.243 -9512.769 -9837.916 -13497.961 -174.225 -17411.627
> 15649.481 -9521.968 -9842.127 -13493.568 -174.517 -17382.699
> 38.238 -9.199 -4.211 4.393 -0.292 28.928
> Potential - Angle - RB = -0.111
> RESULTS FROM TPI
> Using GMX_CAVITY_CENTER cavity
> WARNING: USING CUSTOM CONF FOR INSERTION
> epot = -65.895645
> embU = 21686035981.671570
> F_COUL_RECIP = 0.000000
> F_COUL_SR = -61.993370
> F_LJ = -3.902278
> beta = 0.361176
> BEGIN INSERTED CONFIGURATION
> Frame time: 0.000000
> 14.00 2.058448 1.753919 2.382128
> 1.00 2.116501 1.707533 2.312707
> 12.00 1.961425 1.845027 2.319632
> 1.00 2.037138 1.699207 2.464866
> 1.00 2.021572 1.899345 2.245694
> 12.00 1.895999 1.942494 2.418418
> 1.00 1.896307 1.780891 2.259156
> 1.00 1.853303 1.890639 2.505562
> 1.00 1.961367 2.024441 2.449268
> 16.00 1.780418 1.997807 2.356455
> 1.00 1.751046 2.084993 2.389755
> END INSERTED CONFIGURATION
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João M. Damas
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
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