[gmx-users] Pull code for Constraint

Hi, I try to pull the small molecule from the bulk solution to the surface by the Constraint function. However, it seems that it does not work well. Here my part of run parameters about the Constraint in my mdp file ## constraints = all-bonds; hbonds; all-bonds

[gmx-users] How to calculate the center of the mass in gromacs

Is there the simple method to calculate the center of the mass for a group of atoms? I want to post-process the traj date file. Thanks a lot. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] How to calculate the center of the mass in gromacs

, May 15, 2012, 12:51 PM On 5/15/12 11:35 AM, xu zhijun wrote: Is there the simple method to calculate the center of the mass for a group of atoms? I want to post-process the traj date file. This is a function of g_traj. -Justin -- Justin A. Lemkul

[gmx-users] How to the define the A and B states for the calculation of free energy

Hi gromacs-users, I have carefully checked the manual about the define the A and B states for the calcualtion of free energy. And I also known that couple-moltype“ and couple-lambda0 and couple-lambda1. However I have two types of molecules for decoupling in the simulaiton. It seems that

Re: [gmx-users] How to the define the A and B states for the calculation of free energy

of free energy To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, January 14, 2012, 8:04 PM xu zhijun wrote: Thanks Justin. You mean I put the na+ and Ca+ in the same moleculetype？ But I just worry about whether it is feasible to put the two ions in the same