Re: [gmx-users] REST simulation

Hi Otto, do you know how to use the free energy code in GROMACS for running alchemical transformations (such as thermodynamic integration)? I strongly suggest first to be confortable with that code before trying to implement REST. In such alchemical calculations, you have to specify two topolo

Re: [gmx-users] REST simulation

Hi Patrick, again thanks a lot for your valuable help. But I do not get my head around how to tell grompp that for lambda=0 I would like to use the the unscaled Hamiltonian and for lambda=1 the highest "temperature". In the tutorial the change in temperature is a number which is passed to the pre-p

Re: [gmx-users] REST simulation

Hi Otto, you have to equilibrate at each lambda value! The unscaled Hamiltionian is your lowest "temperature", say 300K, which corresponds to lambda=0. You generate the highest "temperature" by appropriately scaling the Hamiltonian, say 600K, which corresponds to lambda=1. Then you create n di

Re: [gmx-users] REST simulation

Hi Patrick, thanks for your help. What I still do not understand is, how I can set-up the replica simulation starting from the two equilibrated systems. What do I have to put into the .mdp file and in the grompp command to consider the two equilibrated configurations and further obtain the tpr file

Re: [gmx-users] REST simulation

Hi Mark, good to know, this -pp option of grompp is very useful. Thanks! Ciao, Patrick Le 12/12/2011 12:55, Mark Abraham a écrit : On 12/12/2011 8:42 PM, Patrick Fuchs wrote: Hi Otto, in my lab we tried to implement this REST variant in GROMACS as proposed by those authors. We figured out that

Re: [gmx-users] REST simulation

Hi Otto, yes I copied those two files you mentionned (also .rtp for charges) in some specific directory to apply the appropriate scaling. But according to the authors this REST implementation, you just need that for the highest "temperature" (for the lowest, the Hamiltonian is unchanged) and t

Re: [gmx-users] REST simulation

Hi Mark, Thanks a lot. This was very helpful. I have also a question concerning single vs double precision gromacs simulation. Which one is more suitable for this kind of simulation and are there general rules to decide which precision should be used depending on the simulation? All the best Ot

Re: [gmx-users] REST simulation

Hi Patrick, Thanks a lot for your reply. Just to be sure, you create for every replicate a copy of the original force field, and after you manipulate the parameter in ffnonbonded.itp and ffbonded.itp. Then you go for each replicate through the usual simulation preparation steps (minimisation, nv

Re: [gmx-users] REST simulation

On 12/12/2011 8:42 PM, Patrick Fuchs wrote: Hi Otto, in my lab we tried to implement this REST variant in GROMACS as proposed by those authors. We figured out that it was easier to manipulate directly the parameters files in the top directory. There you know exactly what you are doing; recall

Re: [gmx-users] REST simulation

Hi Otto, in my lab we tried to implement this REST variant in GROMACS as proposed by those authors. We figured out that it was easier to manipulate directly the parameters files in the top directory. There you know exactly what you are doing; recall that some interactions (i.e. solvent/solvent

[gmx-users] REST simulation

Dear gromacs users, Recently I stumbled over following paper: T. Terakawa, T. Kameda, and S. Takada, On Easy Implementation of a Variant of the Replica Exchange with Solute Tempering in GROMACS. Journal of Computational Chemistry 32 (2011) 1228-1234. The authors suggested an easy way to run this