Re: [gmx-users] Re: Umbrella Sampling settings

2013-07-12 Thread Justin Lemkul
Friday, July 12, 2013 9:04 PM Subject: [gmx-users] Re: Umbrella Sampling settings In GROMACS groups are called via the *.ndx file (default: index.ndx) Be aware that 'pull_dim' determines in which diretions (x,y,z) the umbrella potential acts. So use N N Y , if you want that the ion can

Re: [gmx-users] Re: Umbrella Sampling settings

2013-07-12 Thread Shima Arasteh
s" (Y). So what should I do?!   Sincerely, Shima - Original Message - From: Thomas Schlesier To: gmx-users@gromacs.org Cc: Sent: Friday, July 12, 2013 9:04 PM Subject: [gmx-users] Re: Umbrella Sampling settings In GROMACS groups are called via the *.ndx file (default: inde

[gmx-users] Re: Umbrella Sampling settings

2013-07-12 Thread Thomas Schlesier
In GROMACS groups are called via the *.ndx file (default: index.ndx) Be aware that 'pull_dim' determines in which diretions (x,y,z) the umbrella potential acts. So use N N Y , if you want that the ion can move freely (onsidering the pull) in the xy-plane and Y Y Y if you want to also restrit th

[gmx-users] Re: Umbrella Sampling settings

2013-07-12 Thread Thomas Schlesier
But you need each of these lines for both cases (SMD and US). Probably one could skip two lines and use the default values, but it's better to set them manually. See below for comments (comments are under the related entry): Thanks for your reply. But when I don't understand why these extra