[gmx-users] PMF calculation using pull code (constraint force method): constrained atom seems to be moving

Dear gmx-users: I am performing a PMF calculation using the pull code. I selected one fixed atom as a reference group and constrained another atom with respect to this reference group so that their separation in the x- and z-directions remain constant. After running the simulation, I visualized th

[gmx-users] Accuracy of force calculation and doubts on PME parameter choice

Dear all: In most studies, we focus on the accuracy of potential energy. How about the force? Consider two systems: 1. Two LJ particles (sigma=0.33nm, epsilon=0.625kJ/mol): If the force is cutoff at 2.5*sigma, so the maximum error in force is at the cutoff length and equal to ~0.08 kJ/mol nm. 2.

[gmx-users] cannot do constraint force run in parallel?

! Is this a problem with the way I am using gromacs or it is a known limitation (unlikely, I feel). Nick -- Forwarded message -- From: Nickle Fan <[EMAIL PROTECTED]> Date: Wed, Feb 27, 2008 at 9:36 PM Subject: inquiry on constraint force run To: [EMAIL PROTECTED] Hi, Beniami

[gmx-users] tabulated potential - why table length is rc+1nm

Dear gmx-users: I am working on incorporating a customized non-bonded interaction into my simulation. I am trying to implementing it through the tabulated interaction potential. The manual says that the potential should be tabulated up to rc+1.0 nm (rc is r_vdw or r_columb). Why is this necessary

[gmx-users] AFM pulling for PMF calculation

Dear gmx-users: I am attempting to calculate the PMF of a small molecule across a membrane. I am using the AFM method (pulling in the z-direction). I find that during the simulaiton, the small molecule moves not only in the pulling direction, but also in the x- and y-direction. Since Pulling_for