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 original---
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 le
Rigid body dynamics for finding
protein folding pathway.
On Sat, Dec 31, 2011 at 10:23 AM, 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 it is not
possible to reproduce
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 it is not
possible to reproduce them (in a reasonable amount of time) on a regular
(super)computer. I think your best shot, if your protein is small enoug
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.
rega
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 user
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, t
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 gene
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 origina
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