I am not sure what you want to measure. You mentioned that "f<span class="Apple-style-span" style="font-family: tahoma, sans-serif; font-size: 13px; border-collapse: collapse; ">orce and energy I calculate are still quite far from the reference values", now are you only looking at electrostatic contributions to these or the total contributions? If its total contribution then LJ parameters should also be correct and for that you should switch to standard gromacs units. </span><div>
<span class="Apple-style-span" style="font-family: tahoma, sans-serif; font-size: 13px; border-collapse: collapse; "><br></span></div><div><span class="Apple-style-span" style="font-family: tahoma, sans-serif; font-size: 13px; border-collapse: collapse; ">Also why do you need to use gmx.ff, seems to me that you already have the parameters (ie the LJ parameters and charges)</span><br>
<br><div class="gmail_quote">On Fri, Jul 29, 2011 at 11:30 AM, Alex Marshall <span dir="ltr"><<a href="mailto:amarsh59@uwo.ca">amarsh59@uwo.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<font face="tahoma,sans-serif">Hi Amit,<br></font><div><font face="tahoma, sans-serif"><br></font></div><div><font face="tahoma, sans-serif">So if I understand you correctly, any LJ interaction I impose on these particles will be quite arbitrary because I'm only concerned with electrostatics, right? How then might I go about comparing the dimensionless reference values given with the values I calculated? I don't think I can simply compare their ratios, as there would still be a unit of length to deal with.<br>
</font></div><div><font face="tahoma, sans-serif"><br></font></div><div><font face="tahoma, sans-serif">Thanks,</font></div><div><font face="tahoma, sans-serif">Alex</font></div><div><div></div><div class="h5">
<div><div class="gmail_quote"><br></div><div class="gmail_quote">On Fri, Jul 29, 2011 at 2:24 PM, Amit Choubey <span dir="ltr"><<a href="mailto:kgp.amit@gmail.com" target="_blank">kgp.amit@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<div><br></div><div>reduced units works for LJ particles only. I am not sure if it works when you include electrostatics. When you set charge = 1 it is 1electronic charge. I would suggest not to use the reduced units for LJ in this scenario.</div>
<div><br></div><div>Amit<br><br><div class="gmail_quote"><div><div></div><div>On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall <span dir="ltr"><<a href="mailto:amarsh59@uwo.ca" target="_blank">amarsh59@uwo.ca</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div>
<font face="tahoma,sans-serif">Hi all,</font><div><font face="tahoma,sans-serif"><br></font></div><div><font face="tahoma, sans-serif">I'm trying to calculate the force on one particle and the total electrostatic energy of my system, which consists of a lattice of 25 evenly spaced charges in the xy plane and a single charge in the center above to preserve charge neutrality. The reference values I have been given are in dimensionless units, so I am tasked with either converting my output to dimensionless units or having gromacs work in reduced units from the get go. I have set the mass of each charge to 1, the magnitude of the charge on each particle to 1, and the values of the C6 and C12 parameters in my itp file to 4.0, since I'm just using gmx.ff for this (hopefully simple) calculation. I've turned off temperature coupling because this is purely a test of the handling of electrostatics with 3D Ewald summation plus the correction for slab geometry. However, the force and energy I calculate are still quite far from the reference values. Have I missed anything if I want my output to be in dimensionless units? </font></div>
<div><font face="tahoma, sans-serif"><br></font></div><div><font face="tahoma, sans-serif">Thanks,</font></div><div><font face="tahoma, sans-serif">Alex</font></div>
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