[gmx-users] g_rotacf

Dear All I have what might be a simple question. For g_rotacf, what is the equation used in the calculation of the rotational correlation function? is there any basic reference one could give me for the same? Also, for the rotational correlation function, is the decay something as simple as the

[gmx-users] g_rdf

Hi GMX ers, I posted this question earlier, but did not receive a reply. Hope to get an answer this time around.I was wondering what could be the origin of a spike at close distances when I compute the RDF of N-P atoms in a lipid bilayer system (0.25 nm) I tried using -cut option and also

[gmx-users] g_rdf again

Dear All I am running a simulation of a DPPC bilayer. I am trying to compute the INTER molecular RDF s of the P-P atoms, N-P atoms and N-N atoms in the head of the bilayer. I have 2 questions,1) When I compute RDF using g_rdf, instead of a getting a smoothly decaying curve at close

[gmx-users] g_rdf again

Dear All I am running a simulation of a DPPC bilayer. I am trying to compute the INTER molecular RDF s of the P-P atoms, N-P atoms and N-N atoms in the head of the bilayer. I have 2 questions, 1) When I compute RDF using g_rdf, instead of a getting a smoothly decaying curve at close

[gmx-users] g_rotacf again

Hello everybody.I have question regarding g_rotacfIf I wanted to compute the rotational correlation function of a linear vector which is between the "centers of masses" of two groups of atoms in an individual molecule (Instead of two atoms), how do I go about it?Can I use g_rotacf to do it ?Thanks

Re: [gmx-users] g_rotacf

g_rotacf with -noaver?Will that compute the rotational correlation of the individual P-N vectors of each lipid molecule and average it over 128 molecules?Thanks in advanceRegardsRamaDavid van der Spoel [EMAIL PROTECTED] wrote: On Fri, 22 Sep 2006, Rama Gullapalli wrote:Hello everybody,I have nearly

Re: [gmx-users] g_rotacf

it over 128 molecules?Thanks in advanceRegardsRamaDavid van der Spoel [EMAIL PROTECTED] wrote: On Fri, 22 Sep 2006, Rama Gullapalli wrote:Hello everybody,I have nearly 100 different vectors to analyse using g_rotacf. I was wondering if there was anyway to do this in GROMACS simultaneously since

[gmx-users] g_rotacf

Hello everybody,I have nearly 100 different vectors to analyse using g_rotacf. I was wondering if there was anyway to do this in GROMACS simultaneously since g_rotacf does not have have the -ng option like in g_traj or others.I would imagine one could use a awk script to run g_rotacf to

[gmx-users] Position of a molecule in a bilayer

Dear GMX ers I would like to compute the position of a small molecule inside a lipid bilayer as a function of its position along the Z axis. Which GMX program is best suited for this? I tried using g_traj, but I got some weird results when i computed the COM position of a DPPC molecule. The COM