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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 try to compute energies of a small peptide-domain complex
and of its constituents using implicit solvent, so that I can get the binding
Delta E. I need the accuracy to be high enough so that I can reliably measure
the Delta Delta E between the wildtype peptide and a mutation of it.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I would like to get advice as to the best setting and parameters
to use; are the ones given below the correct and best ones (most in an mdp file,
some run control parameters of GROMACS commands)? Are other defaults in need to
be changed? <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>As the GBSA method necessitates using the inexact cut-off
interactions, and my system is rather small, I consider using no cut-off at
all, i.e. an all-vs.-all approach. For that I understand the parameters should
be<o:p></o:p></p>
<p class=MsoNormal>nstlist=0<o:p></o:p></p>
<p class=MsoNormal>ns_type=simple <o:p></o:p></p>
<p class=MsoNormal>-pd ; in mdrun<o:p></o:p></p>
<p class=MsoNormal>coulombtype=cut-off<o:p></o:p></p>
<p class=MsoNormal>rcoulomb=0<o:p></o:p></p>
<p class=MsoNormal>vdwtype=cut-off<o:p></o:p></p>
<p class=MsoNormal>rvdw=0<o:p></o:p></p>
<p class=MsoNormal>rlist=0<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Then, there are the implicit solvent parameters themselves:<o:p></o:p></p>
<p class=MsoNormal>implicit_solvent=GBSA<o:p></o:p></p>
<p class=MsoNormal>gb_algorithm= Still<o:p></o:p></p>
<p class=MsoNormal>sa_algorithm=Ace-approximation<o:p></o:p></p>
<p class=MsoNormal>rgbradii=0<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Finally, regarding the simulation box, I see no need for
periodic boundary conditions, and I pick some big margin around the system (as
there are no water molecules, no need to spare):<o:p></o:p></p>
<p class=MsoNormal>pbc=no<o:p></o:p></p>
<p class=MsoNormal>-d 5.0 ; in editconf<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>What do you say?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thanks,<o:p></o:p></p>
<p class=MsoNormal>Ehud.<o:p></o:p></p>
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