Re: [gmx-users] g_cluster warning

On May 14, 2013 2:32 PM, Sabine Reisser sabine.reis...@kit.edu wrote: Hi, I'm having the same warning, would also be interested in what it means. Additionally, I get different results if I use a tpr instead of a gro file in the -s option, using the same trajectory with -f. The results

Re: [gmx-users] g_cluster warning

Hi, I'm having the same warning, would also be interested in what it means. Additionally, I get different results if I use a tpr instead of a gro file in the -s option, using the same trajectory with -f. The results are completely different, for the gro file I get 42 while for the tpr file I

[gmx-users] BUG: Free energy calculation

Dear gromacs users/developers, when trying to couple in a peptide into a membrane with: ; Define position restraints for peptide define = -DPOSRES ; couple in peptide free_energy = yes init_lambda = 0.05 sc_alpha= 0.7 sc_power= 1 couple-moltype = Protein

Re: [gmx-users] BUG: Free energy calculation

for every step. Gromacs version is 4.5.5. I also attached the whole logfile. Cheers Sabine On 03/23/2012 11:52 AM, Mark Abraham wrote: On 23/03/2012 9:17 PM, Sabine Reisser wrote: Dear gromacs users/developers, when trying to couple in a peptide into a membrane with: ; Define

Re: [gmx-users] Umbrella sampling multiple pull groups

Hi, somebody have an idea about this? Cheers Sabine On 03/09/2012 03:52 PM, Sabine Reisser wrote: Hi everyone, I'm trying to fold an unfolded peptide to a helix via umbrella sampling. I've defined 21 pulling groups, the C-Alpha atoms of the peptide, and i am restraining the distance between

[gmx-users] Umbrella sampling multiple pull groups

Hi everyone, I'm trying to fold an unfolded peptide to a helix via umbrella sampling. I've defined 21 pulling groups, the C-Alpha atoms of the peptide, and i am restraining the distance between these groups and the COM of the whole peptide. After the first two steps I used g_wham to create a