Re: [gmx-users] Is there still interest in rigid-body simulation?

Hello, I think it would be very good to have this feature in gromacs. In fact I've recently had some problems with constraining some species in my simulations. Finally I've sorted out with shake but your solution seems to me less problematic. Thanks in advance. Best, Gyorgy Quoting ms

Re: [gmx-users] rigid tetrahedral molecule

Hi Sanku, I've read about your problem just now, I don't know if it's already solved but I had the same problem some weeks ago and I also had a lot of troubles. But, finally I managed to solve it so maybe my experiences can be helpful for you: I think you should use SHAKE instead of LINC

Re: [gmx-users] rigid tetrahedral molecule

Citando David van der Spoel : On 2011-04-29 17.55, gyorgy.han...@fc.up.pt wrote: Hi Sanku, I've read about your problem just now, I don't know if it's already solved but I had the same problem some weeks ago and I also had a lot of troubles. But, finally I managed to solve it so maybe my expe

[gmx-users] energygrps long-range interaction

Dear Users, I'm wondering if it is possible to extract the long-range part of the interactions of energy-groups. In the output I see only short-range terms. I am interested in the total interaction energy of an energy group. I would guess that one should be able to get the long-range par

[gmx-users] angle constrain, constrained PF6 anion

Dear all, I am setting up a simulation of ionic liquids with the PF6 anion. According to the potential, the anion should be kept rigid, wich obviously means that bond lengths and angles have to be constrained. LINCS doesn't work with angle constraints (i.e. constraing a triangle), so we

Re: [gmx-users] angle constrain, constrained PF6 anion

The mdp file is attached. Best, Gyorgy Quoting "Justin A. Lemkul" : gyorgy.han...@fc.up.pt wrote: Dear all, I am setting up a simulation of ionic liquids with the PF6 anion. According to the potential, the anion should be kept rigid, wich obviously means that bond lengths and angles