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On 12/08/2011 12:16 AM, intra\sa175950 wrote:
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<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US">Dear All,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US">Few years ago, C.
Neale (thanks to him!) posted in
the GROMACS mailing list a very useful tutorial [1] to
scale the Coulombic 1-4
interactions when we combine forcefields with different
fudgeLJ and fudgeQQ
values. I am trying to apply this trick to a system
containing a peptide and a
micelle simulated with AMBER99SB-ILDN and GLYCAM force
fields, respectively
(see my previous message [2]). <o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US">I have followed all
the steps described in [2] and
computed the sigma_ij and epsilon_ij values for the
peptide and the micelle
with comb_rules 2 (i.e. sigma_ij=1/2(sigma_i+sigma_j) and
epsilon_ij=sqrt(epsilon_i*epsilon_j). The epsilon_i and
sigma_i are taken from
the [ atomtypes ] section in the ffnonbonded.itp file<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US">However, in the
step 3 in [2], it is said that the
peptide the pair interaction values (i.e. epsilon) should
be divided by 10 and
these "values/12" include in the pairtypes section. I
suspect a typo
here. Indeed, if I set the general fudgeLJ and fudgeQQ to
1.0 and 0.1666666, I
should have a ratio of 10 (for (0.83333/(0.166666)))*1/2
for epsilon_ij and not
"12". Am I right?<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US">To test the
changes, I have performed three nsteps=0
runs in NVT ensemble for a simple system (1 peptide and 1
glycolipid solvated
in water) with the initial and modified and non-modified
nonbonded parameters:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US">1- With
ffnonbbonded.itp file non-modified with
fudgeLJ=0.5 and fudgeQQ=0.83333 --- > peptide<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US">2- With
ffnonbbonded.itp file non-modified with
fudgeLJ=1.0 and fudgeQQ=1.0 --- > micelle<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;" lang="EN-US">3-
With ffnonbbonded.itp file modified with
fudgeLJ=1.0 and fudgeQQ=0.1666666 --- > all</span></font></p>
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</blockquote>
<br>
Using mdrun -rerun allows you to compare more than one configuration
in a run, and avoid any issues associated with bond constraints and
neighbour lists.<br>
<br>
<blockquote
cite="mid:B028D3A83225499589F9136A94D145B4@ceahl0vc8nj6t8"
type="cite">
<div class="Section1">
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US"><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US">and compared the
*.trr files obtained from these the three
runs. <o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;" lang="EN-US">The
only differences I found are, indeed, in the
force section of the *.trr files for atoms involved in the
modified pair
section. To be sure that my modifications are corrects, I
would like to obtain
the individual pair energy values of the micelle and the
peptide. How to obtain
this values? </span></font></p>
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</blockquote>
<br>
Use grompp -pp, and selectively zero out charges and/or VDW
parameters for appropriate [moleculetypes] in the reruns.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:B028D3A83225499589F9136A94D145B4@ceahl0vc8nj6t8"
type="cite">
<div class="Section1">
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US"><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US">[1]
<a class="moz-txt-link-freetext" href="http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html">http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html</a><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US">[2]
<a class="moz-txt-link-freetext" href="http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html">http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html</a><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US">Thank you again for
your help and advices. <o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size:
10.0pt;font-family:Arial" lang="EN-US">Stephane<o:p></o:p></span></font></p>
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