<div dir="ltr">Dear Rui,<div><br></div><div>This interests me and I'd like to help you, but I'm currently swamped.</div><div>I cannot promise it, but I'll try to look at this.</div><div><br></div><div>Regards,</div>
<div>Joćo</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Feb 21, 2014 at 12:28 PM, Rui Fartaria <span dir="ltr"><<a href="mailto:rui.fartaria@gmail.com" target="_blank">rui.fartaria@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<tt>Hi all,<br>
<br>
I am a new user/developer of GROMACS. I am using GROMACS 4.6.3<br>
My goal is to extend the package GromPy, created by René Pool but
I am still new to the code.<br>
<br>
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.<br>
<br>
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:<br>
<br>
</tt>
<ul>
<li><tt>I have a configuration without the inserted molecule and
the same configuration with the molecule inserted.</tt></li>
<li><tt>The molecule in question is monoethanolamine (MEA).</tt></li>
<li><tt>MEA topology was modified with nrexcl=5 so that intra
molecular interactions were not an issue for comparing
insertion energies.</tt></li>
<li><tt>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.<br>
</tt></li>
<li><tt>When calculating the differences between the "inserted"
and "non inserted" configurations I corrected for the
potential energy due to angles and dihedrals.</tt></li>
<li><tt>I hacked the tpi.c source code and forced it to insert the
same configuration as in the tests described above.</tt></li>
</ul>
<p><tt>I prepared at tgz with the tests and the code for the hacked
tpi.c. I can be downloaded from:<br>
<a href="https://www.dropbox.com/s/0lnjancduzi2frf/example_to_send.tgz" target="_blank">https://www.dropbox.com/s/0lnjancduzi2frf/example_to_send.tgz</a><br>
</tt></p>
<p><tt>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 too):<br>
</tt></p>
<tt><br>
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
done.<br>
<br>
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.<br>
<br>
I would be really thankful if someone could help me understand
where the problem is. Hopefully you already know.<br>
<br>
Kind regards,<br>
<br>
Rui Fartaria <br>
<br>
<br>
<br>
Angle RB LJ Coul(SR) Coul(RECIP) Potential<br>
15611.243 -9512.769 -9837.916 -13497.961 -174.225 -17411.627
<br>
15649.481 -9521.968 -9842.127 -13493.568 -174.517 -17382.699
<br>
38.238 -9.199 -4.211 4.393 -0.292 28.928
<br>
Potential - Angle - RB = -0.111<br>
<br>
<br>
******************************************<br>
RESULTS FROM TPI<br>
******************************************<br>
Using GMX_CAVITY_CENTER cavity <br>
<br>
<br>
<br>
<br>
WARNING: USING CUSTOM CONF FOR INSERTION<br>
<br>
<br>
epot = -65.895645<br>
embU = 21686035981.671570<br>
F_COUL_RECIP = 0.000000<br>
F_COUL_SR = -61.993370<br>
F_LJ = -3.902278<br>
beta = 0.361176<br>
BEGIN INSERTED CONFIGURATION<br>
Frame time: 0.000000<br>
14.00 2.058448 1.753919 2.382128<br>
1.00 2.116501 1.707533 2.312707<br>
12.00 1.961425 1.845027 2.319632<br>
1.00 2.037138 1.699207 2.464866<br>
1.00 2.021572 1.899345 2.245694<br>
12.00 1.895999 1.942494 2.418418<br>
1.00 1.896307 1.780891 2.259156<br>
1.00 1.853303 1.890639 2.505562<br>
1.00 1.961367 2.024441 2.449268<br>
16.00 1.780418 1.997807 2.356455<br>
1.00 1.751046 2.084993 2.389755<br>
END INSERTED CONFIGURATION<br>
<br>
</tt><tt></tt>
</div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>Joćo M. Damas<br>PhD Student<br>Protein Modelling Group<br>ITQB-UNL, Oeiras, Portugal<br>Tel:+351-214469613
</div>