Re: [gmx-users] configuration does not change in minimization trajectory

2009-05-01 Thread Justin A. Lemkul
heiko...@web.de wrote: -Ursprüngliche Nachricht- Von: "Justin A. Lemkul" Gesendet: 01.05.09 03:10:01 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] configuration does not change in minimization trajectory heiko...@web.de wrote: Hello all, I am doing a cg minimi

Re: [gmx-users] configuration does not change in minim ization trajectory

2009-05-01 Thread heiko252
> -Ursprüngliche Nachricht- > Von: "Justin A. Lemkul" > Gesendet: 01.05.09 03:10:01 > An: Discussion list for GROMACS users > Betreff: Re: [gmx-users] configuration does not change in minimization > trajectory > > > heiko...@web.de wrote: > > Hello all, > > > > I am doing a cg minim

[gmx-users] position restrain Software inconsistency error: Some interactions seem to be assigned multiple times

2009-05-01 Thread Creighton Buie
Hello Gromacs Community, I am trying to set up a system where there is a coarse grained hydrophobic polymer floor in a solvated water box. I am using the martini force field with an .itp file for the polymer. The "floor" is basically the polymer spaced 0.5 nm apart from each other and the bott

[gmx-users] buckingham and LJ

2009-05-01 Thread Matthew Watkins
Dear all, I would like to use a force-field that includes both Buckingham and LJ non-bonded interactions. I think this cannot be done in an absolutely straightforward way, but please correct me! If it is not possible can the LJ interaction be included as a user specified potential whilst s

Re: [gmx-users] energy xvg file shows a large energy change from time step 0 to time step 0.2 ps

2009-05-01 Thread Justin A. Lemkul
Halie Shah wrote: Hi! I have just completed a position restrained dynamics run on my protein with GROMACS 3.3.3 and I generated an xvg file with the g_energy command...I noticed in this that the energy for time step 0 was 0.88 (near 0) kj mol/S-1/N while the energy for time step 0.2ps was

Re: [gmx-users] Coarse graining for Benzene and related molecules

2009-05-01 Thread Xavier Periole
On Thu, 30 Apr 2009 13:40:58 -0500 ROHIT MALSHE wrote: Hi all, I want to simulate a molecule which has many benzene rings attached to each other. However I want to coarsegrain the system a lot !! Did you look at the Martini CG force field. It should be help full. You can google it. I want