Re: [gmx-users] Accelerated MD in GROMACS

Ok, let's look on the things from another perspective: Using Martini CG model I am modeling protein-protein binding initially putting both proteins on the distance which is much bigger than electrostatics and other non-bonded cut-offs defined by the force field. I need simple, path in-depended

Re: [gmx-users] Accelerated MD in GROMACS

On Tue, Jul 5, 2016 at 3:56 PM, James Starlight wrote: > Hi Mark, > > amd + martini is very popular aproach used by biologists and > biothechnologist becasue of its simplicity compared to umbrella > sampling or IT, What about simplicity vs robustness? Robustness is one

Re: [gmx-users] Accelerated MD in GROMACS

Hi, What do you mean by "it gives more predicable results compared to flooding"? I was actually going to propose that option. If anything, the flooding potential applied in conformational flooding is more meaningful than a non-specific boost potential (to the dihedral and/or total potential)

Re: [gmx-users] Accelerated MD in GROMACS

Hi Mark, amd + martini is very popular aproach used by biologists and biothechnologist becasue of its simplicity compared to umbrella sampling or IT, alternatively it gives more predicable results compared to flooding which has implemented in Gromacs. Finally the aMD is much easily calibrated

Re: [gmx-users] Accelerated MD in GROMACS

Hi, Absolutely. It's merely a question of prioritising limited resources. For example, one has to be able to answer "why should one use aMD rather than AWH?" in order to consider implementing a new method. Then it has to impact a bunch of people, or be immediately useful to the developer / their

Re: [gmx-users] Accelerated MD in GROMACS

Hello Mark, probably to implement of aMD in Gromacs will be very good as well: it will allow to use this protocol with the CG martini systems - where to accelerate sampling of diffusion using double boost approach of amd seems very attractive option for modeling of protein-protein binding for

Re: [gmx-users] Accelerated MD in GROMACS

Hi, In general, one should look at the release notes of software to see what new features were added in a version. This will tend to be findable with Google also :-) Accelerated MD has never been implemented to my knowledge. It would probably be fairly easy, but so far nobody with a suitable

[gmx-users] Accelerated MD in GROMACS

Dear Gromacs users! I wonder t ask whether the aMD was implemented within GMX-5 ? I am looking for the non-equilibrium md protocol with the possibilities to apply one or two boosts on the system to accelerate some diffusion events within it. Thanks ! James -- Gromacs Users mailing list *

Re: [gmx-users] Accelerated MD

Hi Doug, I recently read a good review on ABF http://pubs.acs.org/doi/abs/10.1021/jp506633n. It's focused on ABF but there's a section which compares ABF to other techniques. While I'm at it, are there any plans from gromacs devs to implement ABF in gromacs? Best, Patrick Le 20/10/2014

[gmx-users] Accelerated MD

Hi all, Can anyone recommend a book or (preferably) review article summarising the various accelerated MD methods commonly used in protein/peptide simulation these days? e.g. ABF, PLUMED, REMD, aMD etc. etc. I can read about each individually but I could use a comprehensive but concise