[gmx-users] g_rdf normalization

Dear fellow Gromacs users Does anyone know how the "-surf mol" option works? I am trying to calculate the coordination number for a molecule in a slice (xy-plane, delta-z ~ 0.5 nm) of my system. I believe I understand how to do the integration of the RDF function if I use the center-of-mass opti

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

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

gmx-users-boun...@gromacs.org [mailto:gmx-users-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

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

...@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

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

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 oxygen atom in water 2) between the carboxyl oxygen atoms in

RE: [gmx-users] editconf and g_rmsdist

Dear Tsjerk, Thanks for your suggestion. I tried changing the box values, and it still give a deviation, so I have filed a bug report. Best regards, Soren -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Tsjerk Wassenaar Sent

RE: [gmx-users] all-bonds

: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Wednesday, September 23, 2009 3:51 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] all-bonds Enemark Soeren wrote: > Dear GMX-users, > > Is it possible to exclude a gro

[gmx-users] all-bonds

Dear GMX-users, Is it possible to exclude a group of atoms or molecules from having their bonds converted to constraints when using the all-bonds mdp-option? Best regards, Soren ___ gmx-users mailing listgmx-users@gromacs.org http://lists.groma

[gmx-users] editconf and g_rmsdist

Dear GMX-users I have a question about what happens when editconf is used to "box" a molecule. The reason I ask is because, I have used g_rmsdist in order to study how a very small piece of a structure (100+ atoms) relaxes towards its native state (given by NMR) after a small perturbation.

RE: [gmx-users] generate pair list and 1-4 interactions

Hi Berk, Thanks for your answer, I am happy to have the priority list for how the van der Waals term of the pair potential is calculated. About fudgeQQ, do you mean that the pair potentials' coulomb terms are scaled with the fudgeQQ value, even when "gen-pairs" is set to "no"? ( I see from th

[gmx-users] generate pair list and 1-4 interactions

Dear all, I am a bit confused about how the pair potentials (PPs)are calculated. If I state explicitly sigma and epsilon values for the pair potentials, can I then still have a coulomb scaling of my 1-4 interactions? Say I set "gen-pairs" to "yes", although I have all possible pair potential

RE: [gmx-users] diffusion, g_msd and trestart

-Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: Monday, July 27, 2009 5:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] diffusion, g_msd and trestart Enemark Soeren wrote: > D

RE: [gmx-users] diffusion, g_msd and trestart

-Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: Monday, July 27, 2009 5:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] diffusion, g_msd and trestart Enemark Soeren wrote: > D

[gmx-users] diffusion, g_msd and trestart

Dear all, I am trying to calculate diffusion coefficients for a system of (30) glycine molecules in a box with (1000) water. After running: g_msd -f md.xtc -s md.tpr -mol -n molindex.ndx I get a list of diffusion coefficients - one for each glycine molecule. I then calculate the average a