Re: [gmx-users] Re: Gromacs analysis tools for Namd output

Hu Paul, it is possible the dl library (containing the function to dinamically loading libraries) is missed. To confirm this hypotesis, try: ldd path_g_rmsf On my PC this is the output: linux-vdso.so.1 => (0x7fff6000) libgmxana.so.6 => /apps/gromacs/4.5.5/gnu/lib/libgm

Re: [gmx-users] Re: Gromacs analysis tools for Namd output

Hey Paul, cant help you with the plugin issue, but have you instead tried loading the dcd trajectory into vmd and save it as trr? Cheers, Micha On 7 Feb 2012, at 18:18, "PAUL NEWMAN" mailto:paulcliz...@gmail.com>> wrote: Dear Gromacs users, This is my second email since I tried the previous

[gmx-users] Re: Gromacs analysis tools for Namd output

Dear Gromacs users, This is my second email since I tried the previous advises and did NOT work. I want to use the Gromacs analysis tools for analyzing Namd output files (*.dcd files) I installed Gromacs 4.5.4 (64 bits) and it works well. In addition I installed VMD 1.9 (64 bits) and set up VMD_P

Re: [gmx-users] rotational diffusion for non-globular proteins

Hello, My take on g_rotacf is that calculates the correlation times for a globular proteins that basically the moments of inertia can be assumed to be the same in all directions. Then, a single diffusion constant can be calculated for the whole protein. What if your protein is for instance a single

Re: [gmx-users] g_rdf

Steven Neumann wrote: Hi Gmx Users, I am interested in RDF of my protein resdiues away from the given point in a range of 10 nm. g_rdf provides mi the data for app.5 nm. Is there any chance to change it? The range of the RDF is determined by the box size. You can use g_rdf -nopbc to g

[gmx-users] g_rdf

Hi Gmx Users, I am interested in RDF of my protein resdiues away from the given point in a range of 10 nm. g_rdf provides mi the data for app.5 nm. Is there any chance to change it? Thank you Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] harmonic distance restraints

francesca vitalini wrote: Hi all, I'm sorry for the dumb question but I need to put harmonic restraints on my peptide and I cannot find the right command. So, looking on the how tos link in the gromacs website I understand that I need to add to my topology file a posre.itp file with the sect

Re: [gmx-users] problem with topology generation of ligand

On 7/02/2012 10:52 PM, Anushree Tripathi wrote: How to change parameters of JZ4 topology (as given in tutorial).I think the explaination is given in the article ( Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies) which is not freely available.Please help me. Th

[gmx-users] harmonic distance restraints

Hi all, I'm sorry for the dumb question but I need to put harmonic restraints on my peptide and I cannot find the right command. So, looking on the how tos link in the gromacs website I understand that I need to add to my topology file a posre.itp file with the section [ distance_restraints ] speci

[gmx-users] problem with topology generation of ligand

How to change parameters of JZ4 topology (as given in tutorial).I think the explaination is given in the article ( Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies) which is not freely available.Please help me. -- gmx-users mailing listgmx-users@gromacs.org htt

Re: [gmx-users] overheating problem

Hi, I put a new cooler (Thermaltake Friock) on the CPU. The problem is solved. 2012/2/4 Mark Abraham > On 4/02/2012 11:15 PM, ahmet yıldırım wrote: > > Hi, > The problem might caused by X58 chipset. > Now I am using ubuntu. Which operating system do you recommend? > > > I doubt it is relevant