Re: [gmx-users] Umbrella sampling along Radius of gyration

Hey Chris, It is actually not necessary to go to the code. You can do that by compiling a version of gromacs including the plumed path for free energy calculations. Amogst the several collective variables included there there is gyration radius. Regards Felipe Mensaje

Re: [gmx-users] Re: Folding rate

Actually i know people using Go-models to study protein folding for proteins as large as 300 aa. Now, in these cases you need to use biasing potentials and not temperature exchages (maybe both?). In principle, the REMD will help you with the comformational exchange but it also includes a new

Re: [gmx-users] Re: Folding rate

with Rigid body dynamics for finding protein folding pathway. On Sat, Dec 31, 2011 at 10:23 AM, felmer...@uchile.cl felmer...@uchile.cl wrote: I small thing to consider with that particular paper is that DE Shaw has a special machine (Anton) to do those calculations, so in principle

Re: [gmx-users] RMSD

In any case, if you really want to see flexibility then you need RMSF and not RMSD as the later will only tell you about how similar is the configuration of a sidechain compared to a reference frame. If that is still what you want i think VMD has a tool for that in the timeline plugin.

Re: [gmx-users] more than 100% CPU

Indeed, gromacs (non-mpi) will use all the resources available. If you do not want that you can control de number of threads created with the -nt option of mdrun. regards Felipe Mensaje original De: wgal...@ualberta.ca Fecha: 18-ago-2011 19:26 Para: Discussion list for GROMACS

Re: [gmx-users] which chain to select for MD simulation

Hey, I agree it was unclear, but i guess he meant that he has a crystal structure with two molecules in the asymmetric unit where he knows that the protein is a monomer in solution. Otherwise the question does not even make sense as you pointed out. If it is indeed the asymmetric unit thing,

Re: [gmx-users] Can't unfold the protein

Hey, NPT is not the appropriate way to do this kind of simulations. I am not sure whether or not the water models available for classic MD simulations are able to reproduce the phase behavior. Indeed what you see when your system explodes and gets huge is the water evaporating. What is

Re: [gmx-users] Transition path sampling

Hey, You could use the path collective variables included in PLUMED (you have to compile it with gromacs) or maybe if you know an eigenvector that describes the motion you are interested in (from PCA for instance) you could do some floodin through it. best Felipe Mensaje