[gmx-users] Virtual sites parameters

is of type H and atom 39, 37 and 51 of type C and should be are directive similar to [ bondtypes ] but for virtual site. Does this directive exist ? I had no luck checking the manual. Best regards, Bastien Loubet -- View this message in context: http://gromacs.5086.x6.nabble.com

[gmx-users] Re: pullx file content with pull_geometry = position

I update the post to say that we tried to make a rerun of the trajectory on our local machine and the output of the pullx.xvg file (created with the option -px of mdrun) is: # This file was created Wed Jun 5 12:15:49 2013 # by the following

[gmx-users] pullx file content with pull_geometry = position

around the pull_init1 vector as defined in the mdp file. More importantly these results are different from the results in the pullx.xvg file (at least the results I expected to have). Can somebody clarify what is actually in the pullx.xvg file ? Best, Bastien Loubet -- View this message

[gmx-users] Lipids and virtual site in 4.6.1

Dear GROMACS user, Last week I was watching the GTC talk from Eric Lindahl, and I noticed his insistence on virtual site to accelerate simulation (up to 5ps time step). As a matter of fact our group recently tried to use virtual site on CHARMM36 POPC bilayer and the result where less than

[gmx-users] Re: Lipids and virtual site in 4.6.1

Actually we did not increase the time step between the simulations. The plan was to increase it after we checked the basic properties of the membrane, but we never got to that point. I will try to put something together for redmine soon. Thanks for the answer, Bastien -- View this message in

[gmx-users] virtual sites with CHARMM lipids

in the GROMACS manual (3fd, 3fda, 3out, N) but none of them seems to correspond to the CH2 groups in the carbon chains. It would require an out of plane virtual site with fixed length (so using normalized vector). Can you help me with that ? Thanks, Bastien Loubet -- View this message in context: http

[gmx-users] Re: Possible bug in the temperature calculation from rerun

, maybe I should post my mdp top and log files here or on the developers forum ? Have a good day, Bastien Loubet -- View this message in context: http://gromacs.5086.n6.nabble.com/Possible-bug-in-the-temperature-calculation-from-rerun-tp5001194p5001508.html Sent from the GROMACS Users Forum

[gmx-users] Possible bug in the temperature calculation from rerun

differences between the two topologies and the velocities are draw from the same trr trajectory file. Any thought on this problem would be welcome. Cheers, Bastien Loubet -- View this message in context: http://gromacs.5086.n6.nabble.com/Possible-bug-in-the-temperature-calculation-from-rerun

[gmx-users] Re: Possible bug in the temperature calculation from rerun

Justin Lemkul wrote On 9/21/12 8:29 AM, Bastien Loubet wrote: Dear gmx users, We recently got a problem with the rerun feature of mdrun, and we request your help in order to help to solve it. We have run a simulation of a large POPC membrane using the coarse grained Martini force fields