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<p class=MsoNormal>Dear GROMACS users,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I am hoping to get some information from you experts
regarding the use of user-defined potentials (table*.xvg). With the help
of the GROMACS manual and several posts in the mailing list, I have been able
to make user-defined potential functions that I would like to apply to a system
of small molecules (16 atoms each, ~100 molecules). The crux of the
problem (see below) is that I would like to apply **separate** user-defined
potentials for *intra* and *inter* molecular interactions **<b>in a
computationally efficient way</b>**. The molecule I’m simulating
(in united-atom representation) is:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>C1 – O1 – C – C – O2 – C2<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>and I want:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>(1)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>a user defined potential applied between C1 and C2 on the
same molecule<o:p></o:p></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>(2)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>a different user defined potential between C2 and O1 (&
C1 and O2) on the same molecule<o:p></o:p></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>(3)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>a normal gromacs table potential applied between C1 and
C2 on *<b>different</b>* molecules<o:p></o:p></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>(4)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>a normal gromacs table potential applied between C2 and
O1 (also C1 and O2) on *<b>different</b>* molecules<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I can do this by defining a large number of ‘energygrps’;
specifically I need 4 different ‘energygrps’ for each molecule (i.e.
separate ones for ‘C1’, ‘C2’, ‘O1’, &
‘O2’, with all other atoms lumped into a single ‘energygrp’
for all molecules). Because my simulation system currently contains 91 molecules
this results in 365 ‘energygrps’ in the *.mdp file. Since
this is a lot of ‘energygrps’ I redimensioned the gromacs arrays in
order to handle it as noted previously in the mailing list:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><a
href="http://www.gromacs.org/pipermail/gmx-users/2007-October/030084.html">http://www.gromacs.org/pipermail/gmx-users/2007-October/030084.html</a><o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>This works great but **<b>here’s the problem</b>** : <b>the
simulations run exceedingly slow when I use such a high number of defined ‘energygrps’</b>.
Without using the user defined potential functions I was getting roughly
25 ns/day (which, as always with GROMACS, is amazingly fast!). With
the applied potential functions and ‘energygrps’ however I am only getting
1.5 ns/day. I thought one problem might be the number of times that
‘mdrun’ spends writing to the energy (.edr) file, but I have ruled
this out as a possibility because when I increased my ‘nstenergy’
in my *.mdp file by 100 fold ‘mdrun’ still runs at the same slow rate.
The slowdown therefore appears to be directly related to the number of ‘energygrps.’.
To confirm this, I decreased the number of ‘energygrps’ to 3 (by
lumping all ‘C1’ and ‘C2’ atoms together into one ‘energygrp’
and all ‘O1’ and ‘O2’ atoms into another ‘energygrp’)
and this accelerated the simulations dramatically; however, the same user
defined potential functions are then applied to both **intra** and **inter**molecular
interactions, which is not what I want!<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>If anyone has any suggestions for speeding up the simulations
I’d really appreciate hearing from you!<o:p></o:p></p>
<p class=MsoNormal>Thanks in advance for your help. Any and all comments are
appreciated :)<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Eli Musselman<o:p></o:p></p>
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