Thanks again David.<br>
tpbconv was very useful instead of re-running the simulations and I
could find the dipole moment of the two groups separately and very
quickly ..........<br>
I have one more quick question related to this course of emails about g_dipoles.<br>
Once dipole moment of some biomolecule is calculated, what is a better
way of finding the permittivity of such cluster of homogeneous
molecules.<br>
In a better sense, did anyone tried to find the permittivity of the
lipid tails using gromacs??. I know g_dielectric command can help
one to find permittivity, but I find more appropriate and easier if I
calculate dielectric constant from dipole moment using <a name="1079fdd3cdc88e6a_SECTION00038000000000000000">Clausius-Mossotti relation</a>. <br>
I just wanted to know how to find permittivity of such complex, and are
there any other equations which helps me to find the permittivity of
lipids(without headgroups)??<br>
Best regards,<br>
Viswam.<br>
<br>
<br>
<br>
<span class="q" id="q_1079fdd3cdc88e6a_1"><br><br><div><span class="gmail_quote">On 11/15/05, <b class="gmail_sendername">David</b> <<a href="mailto:spoel@xray.bmc.uu.se" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Tue, 2005-11-15 at 14:33 -0500, Viswanadham Sridhara wrote:<br>> Thanks David.<br>> One more quick question.<br>> g_dipoles takes the molecule number unlike atom number for g_density.<br>> So if I ran a simulation, is there any way out later to divide the
<br>> molecule into 2 seperate entities and find the dipole moment for these<br>> 2 entities.<br>> In other words if i ran the simulation with one kind of molecule which<br>> has a head and tail, and later I want to seperately calculate the
<br>> dipole moment for the head and for the tail, is there any other way<br>> instead of re-running the entire simulation by dividing these two<br>> groups.......<br>> (((( A has B and C entities, I want to find the dipole moment of B
<br>> and C separately. ))))<br>> I hope my question is clear...<br><br>As with perl, there are many ways to do things. Finding out how many is<br>left as an exercise for the reader.<br><br>To start of with, you can use tpbconv to create a tpr file in which all
<br>but the charges your are interested in are zero. Note that you want<br>neutral groups, otherwise the meaning of the dipole is undefined.<br><br>A second, somewhat more difficult possibility is to make a new topology<br>
with different molecule definitions.<br><br><br>> Thanks,<br>> Viswam.</blockquote></div></span>