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<p class=MsoNormal>Dear All,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I am confused about the proper choice of non-bonded
parameters for simulating the CHARMM force field in GROMACS. With other
packages I use VDW-switch and PME with both VDW and the direct space coulomb
cut-off at 1.2 and a neighbor-list cut-off of 1.4. The requirement in
GROMACS that rlist=rcoulomb seems to make that parameter set impossible (unless
one uses PME-switch, which is recommended against in the manual and not
consistent with the original force field parameterization). I have seen a suggestion
to use rvdw=rcoulomb=rlist=1.2, but grompp complains unless rlist<span
style='color:#1F497D'>></span>rvdw under VDW-switch. That seems like a
reasonable complaint, but I am new to GROMACS and wonder if I'm missing
something. What is the recommended set of non-bonded parameters?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thanks in advance,<o:p></o:p></p>
<p class=MsoNormal>Mike Hagan<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas'>---------------------------------------------------------<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas'>Physics
Department<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas'>Brandeis
University <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas'><a
href="http://www.brandeis.edu/departments/physics/hagan/index.html">http://www.brandeis.edu/departments/physics/hagan/index.html</a><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas'>---------------------------------------------------------<o:p></o:p></span></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
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