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On 4/21/2011 10:33 AM, Mark Abraham wrote:
<blockquote cite="mid:4DAF7B66.7020504@anu.edu.au" type="cite">
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On 4/21/2011 10:17 AM, Sanku M wrote:
<blockquote
cite="mid:511424.66866.qm@web114202.mail.gq1.yahoo.com"
type="cite">
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<div style="margin: 0px;">Hi,</div>
<div style="margin: 0px;"> I was trying to calculate the <span
class="yshortcuts" id="lw_1303345020_0">dipole moment</span> of
part of my peptide. In other words, if I have a
10-residue peptide, I was interested in calculating the
dipole-moment contribution of the backbone. So, I made
an index file which have a group containing backbone
atoms. But, if I try to use g_dipoles to get the dipole
moment contribution from the backbone atoms, using
following command:</div>
<div style="margin: 0px;">g_dipoles -s -f traj -n
index.ndx</div>
<div style="margin: 0px;">I get an error :</div>
<div style="margin: 0px;">
<div style="margin: 0px;">-------------------------------------------------------</div>
<div style="margin: 0px;">Program g_dipoles_mod_4mpi,
VERSION 4.0.5</div>
<div style="margin: 0px;">Source code file:
gmx_dipoles.c, line: 1173</div>
<div style="margin: 0px;"><br>
</div>
<div style="margin: 0px;"><span class="yshortcuts"
id="lw_1303345020_1">Fatal error</span>:</div>
<div style="margin: 0px;">index[1]=197 does not
correspond to the first atom of a molecule</div>
<div style="margin: 0px;">-------------------------------------------------------</div>
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</blockquote>
<br>
Calculating a dipole moment of a possibly-charged species requires
that there be a reference point, which is conventionally the
center of mass of the molecule. This means all the atoms of the
molecule have to be known, and g_dipoles assumes the index group
consists of whole molecules.<br>
<br>
So to do the partition you want, you will need to provide the same
molecules, but with zero charges on the non-backbone atoms. That
will mean making a copy of your .top and hacking those charges to
zero to generate a new such .tpr.<br>
</blockquote>
<br>
Actually, tpbconv has the ability to set the charges of a group in a
.tpr to zero.<br>
<br>
Mark<br>
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