[gmx-users] scaling of replica exchange

Dear all, I am making some tests to start using replica exchange molecular dynamics on my system in water. The setup is ok (i.e. one replica alone runs correctly), but I am not able to parallelize the REMD. Details follow: - the test is on 8 temperatures, so 8 replicas - Gromacs version 4.5.3

Re: [gmx-users] scaling of replica exchange

Sorry Luca, my mistake in writing. I used actually 2048. Valeria On Wed, 23 Feb 2011, Luca wrote: Hi Valeria, Dear all, I am making some tests to start using replica exchange molecular dynamics on my system in water. The setup is ok (i.e. one replica alone runs correctly), but I am not able

Re: [gmx-users] scaling of replica exchange

raham wrote: On 02/23/11, Valeria Losasso wrote: Dear all, I am making some tests to start using replica exchange molecular dynamics on my system in water. The setup is ok (i.e. one replica alone runs correctly), but I am not able to parallelize the REMD. Details f

[gmx-users] g_cluster: optimal cutoff

... Any hint? Thanks a lot, Valeria Valeria Losasso v.losa...@grs-sim.de German Research School for Simulation Sciences GmbH 52425 Jülich | Germany Tel +49 2461 61 8934 Web www.grs-sim.de Members: Forschungszentrum Jülich GmbH | RWTH Aachen University Registered in the commercial register of the

[gmx-users] g_cluster: optimal cutoff

Dear all, for my cluster analysis I am using the g_cluster tool with the gromos method. The problem is that I have to compare the results for system of different lengths, and of course the result of the cluster analysis changes according to the cutoff chosen. So what will be a great choice in thi