On Sat, Oct 26, 2013 at 06:06:59PM -0400, Michael Shirts wrote:
> Hi, all-
>
> Rest essentially scales the solute-solvent interactions, but maintains
> the solute-solute interactions. This can be done solely with
> Hamiltonian replica exchange, which is in 4.6. It's a bit tricky,
> though. We pl
Hi
Ive been looking for a sample input for a REST simulation but
so far have not been able to find one.
Does anybody have an example to share?
Ive seen the tutorial by Mark which mentions REST but I dont
see this included in the archived examples.
Am I missing something?
Thanks for any help
Hi,
I have performed a REMD simulation of a protein and ligand in water
as usual the protein and ligand get separated by symmetry operations
however attempts to fix this using trjconv and the standard recipes
(eg. -pbc whole, -pbc nojump) do not appear to be working
in particular after using
>
> This means that although the minimization was run in double precision,
> the atomic configuration is saved in single precision (the last two
> decimal places are not used). Does this mean that each time the
> optimized *.gro file is re-read, it needs to optimize these last two
> decima
>
>Could it be that this, second, compilation might have caused some
>problems -- I had GROMACS compiled in single-precision, and it worked
>fine -- could compiling in double-precision after the initial
>single-precision overrun some files? I'm not sure anymore...
>
from experien
>> See: http://arxiv.org/abs/0803.4060. It might be nice to replace
for those who havent already - download the paper - it contains
a background with all the references you need for thermostats
Andersons "landmark" paper in 1980 (as I gave) - Noses 1984 paper
etc.
David
__
On Tue, Jul 22, 2008 at 11:16:21PM -0400, [EMAIL PROTECTED] wrote:
> Thanks David for sharing your knowledge, especially the note that for
> further information one can refer to the literature that was written
> around the time that these thermostats were released. I have a
> question though:
On Mon, Jul 21, 2008 at 11:46:00PM -0400, Justin A. Lemkul wrote:
>
> I too rely heavily on the Berendsen methods for T- and P-coupling, and have
> always found them satisfactory. I have not seen much beyond the casual
> references to the fact that N-H T-coupling and Parrinello-Rahman P-couplin
On Sun, Feb 24, 2008 at 01:35:51PM +1100, Mark Abraham wrote:
> >
> >Ive been using trjconv but it seems to be failing for a case where the
> >protein switches
> >image in the trajectory but the ligand does not.
>
> Check out trjconv -h, and if none of the options works, please describe
> why th
Hi,
Can anybody tell me what is the best way to re-write a trajectory run with
periodic boundary
conditions such that a molecule (eg. the protein) is chosen as the reference
and every other molecule in the system (eg. ligands) is transformed such that
its periodic
image closest to the referenc
On Thu, Feb 21, 2008 at 02:16:39PM +1100, Mark Abraham wrote:
> David Osguthorpe wrote:
> >Hi,
> >
> >I am having a problem understanding the GROMACS implementation of cutoffs
> >and switching functions - at least Im getting results I cant make sense of.
>
> Ha
Hi,
I am having a problem understanding the GROMACS implementation of cutoffs
and switching functions - at least Im getting results I cant make sense of.
I have been running dynamics of a protein-water system rhombic dodecahedron
periodic boundary system with the twin range cutoff scheme.
I have
12 matches
Mail list logo
