Re: [gmx-users] possible configuration for gromacs gpu compute node

Hi, you can use the mdrun options to reserve specific CPU cores and GPU cards for that run. E.g. if you have two GPUs they will be indexed 0 and 1 so you just say "-gpu_id 0" for one simulation and "1" for the other. For the CPUs it should be sufficient to specify the number of OpenMP threads per

Re: [gmx-users] the complex jump out of box

Hi, there is no "out of the box" when using periodic boundary conditions (PBC). Try using the "-pbc" option of trjconv. See: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Best, Tobias -- View this message in context: http://gromacs.5086.x6.nabble.com/the-complex-

Re: [gmx-users] Implicit solvent simulation of protein folding

UPDATE: I found these parameters to work: http://comments.gmane.org/gmane.science.biology.gromacs.user/52770 Now I have a follow up question. It seems that at 300K my unfolded protein chain quickly collapses into some random conformation and more or less stays that way without much conformationa