Re: [gmx-users] Plumed tutorial
Hi Dinesh and others, I see a few PLUMED tutorials available online, but I wanted to just let anyone know that if they have developed a PLUMED tutorial or are working to create a new one, please feel free to submit any high-quality tutorials to LiveCoMS Journal: https://www.livecomsjournal.org/ I am the Tutorials Lead Editor for LiveCoMS, and we are interested in creating a centralized place for all high-quality, peer-reviewed tutorials for molecular modeling software (either QM or MM). Please contact me if you are interested in submitting a tutorial to us. Thanks, Mala On Mon, May 4, 2020 at 5:37 AM Dinesh Kumar wrote: > Dear gmx users,I am trying to run a protein-ligand simulation using PLUMED > patch.I would like to know if there is a step-by-step tutorial that could > help run metadynamics simulations using PLUMED (like the Gromacs tutorials > already available) > > Dinesh Kumar > > -- > 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. > -- Mala L. Radhakrishnan Associate Professor of Chemistry Director, Biochemistry Program Wellesley College 106 Central Street Wellesley, MA 02481 (781)283-2981 -- 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] Plumed tutorial
Dear gmx users,I am trying to run a protein-ligand simulation using PLUMED patch.I would like to know if there is a step-by-step tutorial that could help run metadynamics simulations using PLUMED (like the Gromacs tutorials already available) Dinesh Kumar -- 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] PLUMED tutorial 2014
Dear gromacs users We are pleased to inform you that we are holding a tutorial and user meeting for PLUMED, which is a small code that can be plugged into gromacs and other MD codes, from the 28th May to the 2nd June of this year in Belfast, Northern Ireland. The first three days of this meeting will be used to train participants on how to use PLUMED 2.0 to analyse and enhance molecular dynamics simulations using state of the art techniques such as umbrella sampling, steered molecular dynamics, metadynamics and replica exchange. There will be a relatively small number of lectures as participants will spend the majority of their time doing hands on calculations using PLUMED 2.0. Practical examples will be taken both from the field of biomolecular modelling and from that of materials science, so application from students working in both fields are encouraged. During the final 3 days of the meeting we will have a user group meeting during which there will be opportunities for more experienced users to come and present the work that they have been doing using PLUMED as well as talks from a number of invited speakers. On top of this there will be three open discussion forums during which all participants can discuss how the code should evolve in the future and what our priorities as a field should be in moving forward. Students interested in biomolecular modelling are also encouraged to apply to the tutorial on CHARMM (http://www.cecam.org/workshop-1043.html) in Dublin that is happening the week after ours in Dublin. The material covered during this meeting compliments the material that will be covered during our tutorial. Applications can be made to attend either the whole PLUMED meeting (tutorial + user group meeting, but NOT the CHARMM tutorial) or to attend just the user group meeting. These applications should be submitted through the website: http://www.cecam.org/workshop-1026.html Accommodation will be available for those participants attending both the tutorial and user group meetings at a cost of at most £200. We are hoping to be able to make a significant contribution towards the accommodation costs of participants so the final price that you will have to pay may well be considerably less than this sum. However, at present our funding situation is uncertain so we cannot guarantee anything. Those participating in only the user group meeting will have to make their own accommodation arrangements. Applications should be submitted before March 15th. We will let you know whether or not you have been successful by April 1st. The plumed developers -- 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.
