RE: [gmx-users] g_rdf and number of atoms to include

2009-10-22 Thread Enemark Soeren
Subject: Re: [gmx-users] g_rdf and number of atoms to include On Thu, Oct 22, 2009 at 05:17, Enemark Soeren wrote: Ahh, now I understand - sorry, Omer! No problem, glad to help. In fact, I have compared all three single hydrogen RDFs and they are identical and also

Re: [gmx-users] g_rdf and number of atoms to include

2009-10-22 Thread Omer Markovitch
On Thu, Oct 22, 2009 at 05:17, Enemark Soeren wrote: > Ahh, now I understand - sorry, Omer! > > No problem, glad to help. > > > In fact, I have compared all three single hydrogen RDFs and they are > identical and also relatively smooth. Since, however, with 3 times more data > points (all thre

Re: [gmx-users] g_rdf and number of atoms to include

2009-10-21 Thread Mark Abraham
-boun...@gromacs.org] *On Behalf Of *Enemark Soeren *Sent:* Wednesday, 21 October 2009 8:28 PM *To:* Discussion list for GROMACS users *Subject:* RE: [gmx-users] g_rdf and number of atoms to include Hi Omer, Thanks for your input. Let me reformulate my problem: I have glycine molecul

RE: [gmx-users] g_rdf and number of atoms to include

2009-10-21 Thread Enemark Soeren
ssion list for GROMACS users Subject: RE: [gmx-users] g_rdf and number of atoms to include Omar's response answered that question on why they are different. In the first one you are grouping all three into one group, second is just one of the hydrogen types. The fact that the rdf you get is

RE: [gmx-users] g_rdf and number of atoms to include

2009-10-21 Thread Dallas B. Warren
emark Soeren Sent: Wednesday, 21 October 2009 8:28 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_rdf and number of atoms to include Hi Omer, Thanks for your input. Let me reformulate my problem: I have glycine molecules in the form of zwitterions: 1ZGLY

RE: [gmx-users] g_rdf and number of atoms to include

2009-10-21 Thread Enemark Soeren
...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Omer Markovitch Sent: Wednesday, October 21, 2009 4:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_rdf and number of atoms to include On Wed, Oct 21, 2009 at 07:28, Enemark Soeren wrote: Dear users, I would

Re: [gmx-users] g_rdf and number of atoms to include

2009-10-21 Thread Omer Markovitch
On Wed, Oct 21, 2009 at 07:28, Enemark Soeren wrote: > Dear users, > > I would like to compare interactions between molecules by using RDF. I have > tried looking at glycine and water, and compare the following two > interactions: > > 1) between the amine hydrogen atoms in glycine and the o