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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear gmx-users:
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<div>I was trying to do a free energy calculation of a charged ligand, according to the paper "Calculation of Absolute Binding Free Energies for Charged Ligands and Effects of Long-Range Electrostatic Interactions ", one of the problems with charged ligands
is that the use of a solvent-solvent cutoff causes an overpolarization of the the solvent toward the solute charge, but this can be done by not using any cutoffs at all (If I did not misunderstand it). </div>
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<div>In the following, this is my part of mdp parameter for non-charged ligand:</div>
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<div>; Neighborsearching and short-range nonbonded interactions</div>
<div>nstlist = 10</div>
<div>ns_type = grid</div>
<div>pbc = xyz</div>
<div>rlist = 1.2</div>
<div>; Electrostatics</div>
<div>coulombtype = PME</div>
<div>rcoulomb = 1.2</div>
<div>; van der Waals</div>
<div>vdw-type = switch</div>
<div>rvdw-switch = 0.8</div>
<div>rvdw = 0.9</div>
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<div>for charged ligand, it is like this:</div>
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<div>; Neighborsearching and short-range nonbonded interactions</div>
<div>nstlist = 0</div>
<div>ns_type = simple</div>
<div>pbc = no</div>
<div>rlist = 0.0</div>
<div>; Electrostatics</div>
<div>coulombtype = cut-off</div>
<div>rcoulomb = 0.0</div>
<div>; van der Waals</div>
<div>vdw-type = cut-off</div>
<div>rvdw-switch = 0.0</div>
<div>rvdw = 0.0</div>
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<div>Is this correct for what it means in the paper that by using no cutoff at all?</div>
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<div>Anyway, I presume that this is correct, and run some free energy calculation, when I used the g_bar to calculate the results, I got the error message like this :</div>
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<div>Fatal error:</div>
<div>Some dhdl files contain only one value (dH/dl), while others </div>
<div>contain multiple values (dH/dl and/or Delta H), will not proceed </div>
<div>because of possible inconsistencies.</div>
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<div>So what does it mean?</div>
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<div>Thank you for answering my questions in advance.</div>
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<div>Regards</div>
<div>Chunxia</div>
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