[gmx-users] Re: umbrella sampling with distances larger than half box size

Thanks Stephan for your suggestions, A finally found a solution for distance larger than half the box size: 1) Regenerate the tpr files with pbc=no 2) Perform WHAM analysis with the umbrella forces (-if) -- View this message in context: http://gromacs.5086.n6.nabble.com/umbrella-sampling-with-d

[gmx-users] umbrella sampling with distances larger than half box size

Dear Users, I am performing umbrella sampling simulations of the ring closure of DNA minicircles. The problem with pull_geometry=distance is that the end-to-end distance used as general coordinate becomes at some point larger than half the box size. The distance to the closest image is us

[gmx-users] A simulation of pure chloroform with AMBER compatible parameters never gives the right density

Dear Users, I am trying to reproduce the results obtained by Fox & Kollman on chloroform presented in the following papers but can never achieve the proper density of 1.459 they obtain with their own rigid CHCL3 model. The best I obtain with the parameters presented below is 1.390. I trie