[gmx-users] xpm2ps help

Dear all, I am working with gromacs 3.3.3 Trying to analyse possible changes in the secondary structure of the peptide along the simulation. do_dssp -f traj.xtc -s topol.tpr -sc -dt 5 1 protein xpm2ps -f ss.xpm There are 1 matrices in ss.xpm Matrix 0 is 20001 x 12 zsh: segmentation fault

[gmx-users] peptide MD

Dear users, Trying to perform a MD for a peptide 12aa long. Following the tutorial for peptides MD: http://www.gromacs.org/documentation/reference/online/speptide.html everything seems fine till I reach PR MD. First I get a warning for grompp: WARNING 1 [file aminoacids.dat, line 1]: T-Coupl

[gmx-users] xpm2ps -f ss.xpm

Dear all, I am trying to generate a postscript file using xpm2ps. I had a look in the archive, where they suggest the use of gimp to visualise ss.xpm. However, for some reason the colour I got with gimp is not the same in ps. And the display with gimp is not colour coded. I can tell by comparing

[gmx-users] mdp files gromacs 3.3

Dear all, I am using gromacs 3.3-1, ff G53a6. When using mdp files, as for example for a relax_md, I got the following error messages: WARNING 1 [file relax.mdp, line unknown]: Unknown left-hand 'bd-temp' in parameter file WARNING 2 [file relax.mdp, line unknown]: Unknown left-hand 'zero-te

RE: [gmx-users] genion - hangs up

Hi Tsjerk Thanks for the mail. I think my machine got the problematic Gromacs version when it underwent a big upgrade since I never manually compiled Gromacs on it. In other words it looks like it got a problematic rpm(/deb etc) via Synaptic(/whatever). Is that possible - can this problem ha

[gmx-users] genion - hangs up

Dear all, I am having problem with genion. I have already search the gmx archive, and got the following message: While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na and it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I thought it might be my system, so