Finally had a look through the gromacs 4.0 source code.
Don't know if this bug/points already have been reported and changed
in 4.0.2:
1) There is never memory allocated for the pointers to the user
defined groups:
mdatoms->cU1 etc.
These pointers will stay NULL when a user defined group i
Dear Ran,
Indeed, strictly speaking a smaller time step will give you a more
precise intergration over phase-space. However, as the CG-model itself
and theirfore its corresponding energy description are parametrized
for only a certain range in time steps. The extra details which one
gains
wit
On Mon, 16 Apr 2007 09:40:58 +0200
lorix <[EMAIL PROTECTED]> wrote:
Hi everybody,
I am simulating a protein (approximately 5000 atoms) in
water (35000 atoms). The protein is out of a
thermodynamic equilibrium because I modified a
crystallographic structure of one of its conformation
(which
On Thu, 5 Apr 2007 18:53:58 +0200
Sang-Min Park <[EMAIL PROTECTED]> wrote:
Dear all,
I calculated the eigenvalues and eigenvectors from a
small peptide with a
closest water neighboorhood watersurrounding.
To do this I generated a new trajectory with the command
"trjorder" to order
the wat
On Thu, 11 Jan 2007 09:50:12 +0800
"Hu Zhongqiao" <[EMAIL PROTECTED]> wrote:
Thanks, Mark and Jelger,
To Jelger,
But If one can run BD by setting integrator=sd, how is
dielectri
constant of water set in the simulation? On p141 of the
Manual v3.3,
there is one option epsilon_r. Does it mean
On Wed, 10 Jan 2007 17:36:10 +1100
Mark Abraham <[EMAIL PROTECTED]> wrote:
Hu Zhongqiao wrote:
Hi,
Nobody implied me till now. So that means the current
version can not do
BD by implicitly treating water into continuum media,
i.e, use of
dielectric constant of water. I hope Gmx developers
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