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
> splitres 3
Splitting group 3 'MIL' into atoms
> splitat 3
Splitting group 3 'MIL' into residues
2006/9/15, Qiao Baofu <
[EMAIL PROTECTED]>:
Hi All
I have 2 questions about using g_rdf -com:
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?
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?
PS: I use gromacs 3.3.1.
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Sincerely yours,
**********************************************
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
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Sincerely yours,
**********************************************
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
**********************************************
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