[gmx-users] Re: Umbrella Sampling Pull code Problem - Follow-Up

Steinbrecher, Thomas (IPC) thomas.steinbrecher at kit.edu
Fri Sep 14 16:30:17 CEST 2012

Dear Gromacs users,

a while ago I have sent out a message regarding different distance measurements in the pull code vs. those made by g_dist. Thanks to everybody who responded and observed the same problem. I am still somewhat puzzled. Several users suggested that this is connected to the 'sign' of the distance and setting the group-COM-distance restraint to +1.95 or -1.95 nm makes a difference. I will try and see what behaviour results from this, but can someone more familiar with the Gromacs source code and algorithm than me weight in and let me know if there really is such a thing as a negative distance in the pull code? If yes, what is the definition of that? Is this behaviour discussed in the manual?

Kind Regards,


Dr. Thomas Steinbrecher
Institut für Physikalische Chemie, KIT
Kaiserstr. 12, 76131 Karlsruhe

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