Re: [gmx-users] DPOSRES and energy minimization

2013-11-04 Thread Justin Lemkul
On 11/4/13 1:31 AM, Gianluca Interlandi wrote: Is there a way to tell from the log file whether positional restraints are really activated or not? Yes, there is a position restraint energy term written to the .log and .edr files if the restraints are active. -Justin -- ==

Re: [gmx-users] DPOSRES and energy minimization

2013-11-03 Thread Gianluca Interlandi
Is there a way to tell from the log file whether positional restraints are really activated or not? Thanks, Gianluca On Sun, 3 Nov 2013, Justin Lemkul wrote: On 11/3/13 12:38 AM, Gianluca Interlandi wrote: Is it possible to use position restraints: define = -DPOSRES during an energ

Re: [gmx-users] DPOSRES and energy minimization

2013-11-03 Thread Justin Lemkul
On 11/3/13 12:38 AM, Gianluca Interlandi wrote: Is it possible to use position restraints: define = -DPOSRES during an energy minimization? I tried to do that but it looks like all atoms are moved during minimization: Depending on the forces present in the system, it is possible that the a

Aw: [gmx-users] DPOSRES and energy minimization

2013-11-03 Thread lloyd riggs
(which seems to keep the protein where I want at this point).   Sincerely,   Stephan Watkins   Gesendet: Sonntag, 03. November 2013 um 05:38 Uhr Von: "Gianluca Interlandi" An: "Discussion list for GROMACS users" Betreff: [gmx-users] DPOSRES and energy minimization Is it poss

[gmx-users] DPOSRES and energy minimization

2013-11-02 Thread Gianluca Interlandi
Is it possible to use position restraints: define = -DPOSRES during an energy minimization? I tried to do that but it looks like all atoms are moved during minimization: ; VARIOUS PREPROCESSING OPTIONS = title= cpp = /lib/cpp include =