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<DIV><FONT color=#000000 size=2 face=Arial>Dear Gromacs users,</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>While I was using Gromos force field in simulating a protein in explicit solvent, I used the following parameters:</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial><STRONG>rcoulomb = 1, rlist =1, rvdw = 1.4</STRONG></FONT></DIV>
<DIV><FONT size=2 face=Arial><STRONG>Electrostatitcs : PME</STRONG></FONT></DIV>
<DIV><FONT size=2 face=Arial><STRONG>VDW : Twin range cutoff</STRONG></FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>The above situation will not allow the calculation of any <STRONG>long-range electrostatics (LR-Coul)</STRONG> while calculating the energy of interaction among the specified energy groups of the the studied system.</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>I am facing the question of to what extent that could affect the accuracy of the calculation of the energy of interaction among the specified energy groups of the the studied system.</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>I argue that electrostatic interaction is mainly composed of H-bonds and salt-bridges, both with distance cutoffs of 0.35 nm and 0.4 nm respectively. So there should not be any need for calculating any electrostatic interaction beyond 1 nm (rcoulomb). </FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2><FONT face=Arial>On the other hand, I came across another argument that calculating the long range electrostatics is <STRONG>"complicated by the practical limitations of dividing lattice sum energies into energy groups"</STRONG>. I could not find any explanation of this point in the Gromacs manual! But I assume this kind of argument could be valid if ignoring the long range electrostatics would drastically affect the accuracy of interaction energy calculations mentioned above.</FONT></FONT></DIV>
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<DIV><FONT size=2 face=Arial>I would appreciate any feedback or comment concerning the above arguments.</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>Thanks a lot</FONT></DIV>
<DIV><FONT size=2 face=Arial>Hassan</FONT></DIV>
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