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<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;
font-family:Arial">Dear GMX users,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;
font-family:Arial"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;
font-family:Arial">I cannot figure out from the manual whether it is possible to use tabulated non-bonded potentials in a BAR calculation. <o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;
font-family:Arial"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;
font-family:Arial">I want to estimate the free energy for changing Fe2+ to Fe3+. These have different charges, of course, and also different non-bonded interactions. These non-bonded
interactions are neither LJ nor Buckingham, so I am using a lookup table (table_O_Fe2.xvg and table_O_Fe3.xvg) for the “vdw” part (vdw_type=User).<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;
font-family:Arial"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;
font-family:Arial">I think I should be able to define Fe2 and Fe3 atoms types, and associate the tables (table_O_Fe2.xvg and table_O_Fe3.xvg) with those types in the mdp file:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;
font-family:Arial"><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:"Courier New"">energygrps = O Si Na Ca Al Fe2 Fe3
<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:"Courier New"">energygrp_table = O Al O Ca O Fe2 O Fe3 O Na O O O Si Si Al Si Ca Si Fe2 Si Fe3 Si Na
Si Si Na Al Na Ca Na Fe2 Na Fe3 Na Na Ca Al Ca Ca Ca Fe2 Ca Fe3 Al Al Al Fe2 Al Fe3 Fe2 Fe2 Fe2 Fe3 Fe3 Fe3
<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span lang="PL" style="font-size:10.0pt;
font-family:Arial"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;
font-family:Arial">and in the .top file:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;
font-family:Arial"><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">[ atomtypes ]<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">;name mass charge ptype A B<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""> </span></font><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:
"Courier New"">O
15.99940 -1.20000 A 0.0 0.0<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:"Courier New""> Na 22.99000 0.60000 A 0.0 0.0
<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:"Courier New""> Si 28.08000 2.40000 A 0.0 0.0<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:"Courier New""> Ca 40.07800 1.20000 A 0.0 0.0<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:"Courier New""> </span></font><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">Al
26.98200 1.80000 A 0.0 0.0<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""> Fe2 55.30500 1.20000 A 0.0 0.0<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""> Fe3 55.30500 1.80000 A 0.0 0.0<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">[ nonbond_params ]<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">; i j func C6 C12
<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""> </span></font><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:
"Courier New"">O
O 1 4.0904959800 2.12268E-09<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:"Courier New""> O Si 1 32.858468400 9.64853E-11<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:"Courier New""> O Na 1 2.2541869930 4.82427E-10<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:"Courier New""> </span></font><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">O
Ca 1 2.9149186000 4.82427E-10<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""> O Al 1 34.887265640 8.68368E-11<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""> O Fe3 1 40.425524240 1.92800E-10<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""> O Fe2 1 7.542 1.92800E-10<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">...<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">Also in the .top file, I define a moleculetype Fe, which is Fe2 in state A and Fe3 in state B:<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">[ moleculetype ]<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">; name nrexcl<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">Fe 0<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">[ atoms ]<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">; nr type resnr residue atom cgnr charge mass typeB chargeB massB<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">1 Fe2 1 Fe Fe 2 1.2 55.3050 Fe3 1.8 55.305<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">I expect that I could specify this atom in the gro file like this:<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">...<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""> </span></font><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:
"Courier New"">1764Na
Na 1764 3.448 3.335 0.801 0.9202 0.1009 -0.6229<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:"Courier New""> 1765Fe Fe 1765 1.123 1.300 0.562 0.3254 -1.0409 -0.6704<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:"Courier New""> 1766Ca Ca 1766 2.536 3.320 1.379 -0.5737 -0.4492 -1.8149<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:"Courier New"">...<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span lang="PL" style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">The problem is that grompp fails, telling me
<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">“<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">Fatal error:<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">Group Fe2 not found in indexfile<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">“<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">So, while I want to associate the tables with atom types, it seems GMX is expecting that I am associating the tables
(through the energy groups) with a particular atom, which, in my case, moves between two atom types in the BAR calculation.<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">Can anyone tell me whether I am just suffering from a misconception about how the tables (or energy groups) are used,
or whether it is in fact just not possible to do BAR (or other free energy) calculations in this way?<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">Thanks
<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New"">Jim Rustad<o:p></o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="text-autospace:none"><font size="2" face="Courier New"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;
font-family:Arial"><o:p> </o:p></span></font></p>
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