<br><br><div class="gmail_quote">On Wed, Dec 1, 2010 at 4:30 PM, Hassan Shallal <span dir="ltr"><<a href="mailto:hshallal@pacific.edu">hshallal@pacific.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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<div><font color="#000000" size="2" face="Arial">Dear Gromacs users,</font></div>
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<div><font size="2" face="Arial">I am trying to use CHARMM27 taking the simulation conditions of two recent articles as guides in optimizing the simulation parameters. </font><font size="2" face="Arial"><strong>(DOI: </strong>10.1021/ct900549r <font color="#0000ff">and</font> <strong>DOI:</strong> 10.1021/jp101581h).
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<div>-- Both are using PME for electrostatics and I am planning to do that too</div>
<div>-- Both have rcoulomb = 1.2 (this value is optimal for CHARMM27 force field as mentioned)</div>
<div>-- In the second paper, they have explicitly assigned rvdw = 1.2 (this value is also optimized for CHARMM27 force field) and they assigned the NS rlist = 1.2 because as I understand, using PME as a coulombtype requires rcoulomb to be equal to rlist. <font color="#0000ff">I have no problem following up until now and it seems that (rlist = rcoulomb = rvdw = 1.2) presents the best combination of cut-offs for using (coulombtype = PME and vdwtype = cut-off) along with CHARMM27</font></div>
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<div>-- What I can't get is that in the first paper, they mentioned the following <font color="#ff0000"><strong>"<font size="2" face="Times-Roman"><font size="2" face="Times-Roman">van der Waals interactions were switched off between 1.0 to 1.2 nm"</font></font></strong></font></div>
<div><strong><font color="#0000ff">what does that mean in terms of cut-offs and vdwtype?</font></strong></div>
<div><font color="#000000">Does that mean <strong>vdwtype = switch</strong>, <strong>vdw_switch</strong> <strong>= 1</strong>, <strong>rvdw = 1.2</strong> ? </font></div></font></div></div></blockquote><div>yes. </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div><font size="2" face="Arial"><div><font color="#000000">and if this is what is meant, then rlist has to be 0.1-0.3 larger than rvdw to accomodate for the size of the charge groups as mentioned in the manual and accordingly, we can't keep rcoulomb = 1.2 because rcoulomb must be equal to rlist to allow using PME.</font></div>
</font></div></div></blockquote><div>CHARMM FF doesn't use charge groups. Thus (as far as I understand) this warning can be ignored. You still miss a few interactions because the neighbor-list only contains everything up to 1.2 thus an atom at a distance just above 1.2 and moves a bit inwards, it is not included until the next neighbor-list update. But because the interaction is already switched it is not very critical in my opinion. If you want to avoid this you can use PME-Switch but this is significant slower.</div>
<div><br></div><div>Roland </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div><font size="2"><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: arial; "> </span></div>
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<div><font size="2" face="Arial"> </font></div><br>--<br>
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