[gmx-users] PCA in dihdral space
Dear Gromacs users! In the tutorial I found that tomake a list for dihedral angles via mk_angndxI need to provide tpr file as an input. Here some of my questions: 1)Is itpossible to make a list from pdb file (or convert pdb to tpr),assuming that my trajectory has been calculated not in Gromacs ? 2) Does this method good forcalculation of PCA of Chi-1 angle of the side chains (e.g to clarifythe contribution of the concerned rotation of the side-chain)? Thanks ! Gleb -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Hyper-threading on multi-CPU xeon worstation
Dear Gromacs users! I wonder to ask whether is possible to expect an increase in Gromacs performance with HT technology on my Xeon cpu (72 cpus without HT and 144 with HT)? How would be better to calibrate mdp options (e.g integrator, adjust electrostatics cut-offs) to obtain best performance from my workstation with enabled HT? Does the HT give better performance in case of simulation of big systems (e.g MARTINI with > 200 of CG particles)? Thanks in advance! Gleb -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] On the modeling of a shear flow
Dear GROMACS Users, I am interesting in the work-flow of the shear flow modeling in GROMACS. I am dealing with a complex MARTINI CG membrane system consisted of several proteins embedded within big POPC-cholesterol bi-layer solvated in non-polarizable water. Within this system I would like to introduce a shear flow in form of a force gradient acting in a specific direction along the X or Y plane resulting in a directed acceleration of water on the surface of the membrane, thus mimicking a flow. I will be grateful for any ideas how this could be modeled in Gromacs e.g special setups for Barostats or more complex cases using steered codes of GROMACS? Thanks in advance! Gleb -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
