Hi,<br>I am using Gromacs 3.3.1. In the help file of make_ndx, it is said that "splitres" is to split group into residues, and "splitat" is to split group into atoms. But after I use them two, I found they are opsite. see the following
example<br><br>> splitres 3<br>Splitting group 3 'MIL' into atoms<br><br>> splitat 3<br>Splitting group 3 'MIL' into residues<br><br><br><br><br><br><div><span class="gmail_quote">2006/9/15, Qiao Baofu <<a href="mailto:qiaobf@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
qiaobf@gmail.com</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>Hi All<br><br>I have 2 questions about using g_rdf -com:
<br>1. In the manual, it is said that when -com option used, the rdf is calculated with respect to the center of first group. My question is that, if i want to calculate the rdf of the COM of two groups, how to do it?
<br>2. In my mind, for single-atom, the COM should just be the center of it. Therefore, if I calculate the rdf of two single-atom groups WITH and WITHOUT -com option, the result should be the same. However, it is not that case. I calculated the rdf of H-Cl in these two methods, and got quite different result!! see the attachment. Why?
<br> <br><br>PS: I use gromacs 3.3.1.<br clear="all"></div><div><span><br>-- <br>Sincerely yours,<br>**********************************************<br>Baofu Qiao, PhD<br>Frankfurt Institute for Advanced Studies
<br>Max-von-Laue-Str. 1<br>
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529<br>**********************************************
</span></div><br clear="all"></blockquote></div><br><br clear="all"><br>-- <br>Sincerely yours,<br>**********************************************<br>Baofu Qiao, PhD<br>Frankfurt Institute for Advanced Studies<br>Max-von-Laue-Str. 1
<br>60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529<br>**********************************************