On 2013-08-07 22:50, 朱文鹏 wrote:
Dear all,
I am trying to set up an all-atom MD simulation to investigate the
interaction between lipid bilayer and infinite substrate of graphene or
graphene oxide. The edge effects of graphene and graphene oxide are not
what I am concerned. The lipid bilayer is
On 2013-08-08 01:16, Golshan Hejazi wrote:
Hello,
I have performed quit a lot of tests and I have some question:
I have an amber.crd and amber.top files ... I perform a single step energy
calculation with amber , gromacs and cp2k. in all of them I am using amber
force field but the point is
Hello David,
Thank you for your response.
Do you mean a finite lipid bilayer on a periodic infinite graphene layer,
or a lipid liposome (or a whole spherical cell) on a periodic infinite
graphene layer?
For the first case, how do you control the surface tension of lipid
bilayer? For the second
On 2013-08-08 13:17, 朱文鹏 wrote:
Hello David,
Thank you for your response.
Do you mean a finite lipid bilayer on a periodic infinite graphene
layer, or a lipid liposome (or a whole spherical cell) on a periodic
infinite graphene layer?
A 2D periodic graphene layer - which will be an
Dear GMX users.
I have done simulation of ions and water near quartz surface
(ClayFF) using GPU (GTX580) and Gromacs (4.6.1, single precision, 64
bit, SSE4.1, fftw-3.3.3) and have observed strange behavior of water
and ions. Its NVT simulation with freezed surface atoms (see .mdp
below) and
Hi,
The -testverlet option is only for testing (as the name implies).
Please set the mdp option cutoff-scheme = Verlet
Also please update to 4.6.3, as this, potential, issue might have already been
resolved.
With the Verlet scheme the CPU and GPU should give the same, correct or
incorrect,
I can confirm this, I have noticed this as well.
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FYI I have done some more experimenting on the problem with different
versions and computers running the exact same start .tpr file and this is
what ive found:
Computer A with 4.6.1 or 4.6.3 with MPI = random energy drops
Computer A with 4.6.1 or 4.6.3 without MPI = no random energy drops
On 8/8/13 11:51 AM, Brad Van Oosten wrote:
FYI I have done some more experimenting on the problem with different
versions and computers running the exact same start .tpr file and this is
what ive found:
Computer A with 4.6.1 or 4.6.3 with MPI = random energy drops
Computer A with 4.6.1 or
On 8/8/13 2:13 PM, Shima Arasteh wrote:
Hi,
Would you please let me know if it is possible to get just the first 2
histograms of total 24 histograms by running g_WHAM?
I mean the tpr-files.dat contains only 2 .tpr files of umbrella sampling
simulations and not the all.
I ran such dat file,
Hi,
Would you please let me know if it is possible to get just the first 2
histograms of total 24 histograms by running g_WHAM?
I mean the tpr-files.dat contains only 2 .tpr files of umbrella sampling
simulations and not the all.
I ran such dat file, but doesn't work and gives me an error of
On 8/8/13 2:37 PM, Shima Arasteh wrote:
g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCalvv
It's the error what get;
File input/output error:
tpr-files.dat
Then a file named tpr-files.dat does not exist in the working directory.
Check for typos and the existence of the
Dear GROMACS users,
I followed the Umbrella Sampling tutorial to run a simple simulation of
pulling polymer chain from the surface of micelle. I used position
restraints for the initial equilibration, however I realized a typo in the
define=-DPOSRES mdp files for pulling, US_NPT and US_MD
On 8/8/13 3:57 PM, rookie417 wrote:
Dear GROMACS users,
I followed the Umbrella Sampling tutorial to run a simple simulation of
pulling polymer chain from the surface of micelle. I used position
restraints for the initial equilibration, however I realized a typo in the
define=-DPOSRES mdp
Hello,
As we're trying to get familiar with Gromacs, in order to be able to
perform solvation free energy calculations of ions, we're trying to
replicate the results obtained by Aqvist (the author of the article from
which were obtained Lennard-Jones parameters for alkaline and alkaline
it more accuratly represents reality (my opinion), but is not feasable with high energy affinities such as protein-protein or DNA-protein interactions with short (under u or m seconds) and is used as such (I assume) in many things, or you cant pull them apart. A comparison however, would probably
Hi All,
I would like to restrain the COM of a molecule, say a protein, in my
simulation. I found the pull code can do the job. However, I am not sure
about several parameters in the .mdp file.
For example, if I want to restrain the COM of the protein in only z
direction, but not rigidly, I can
On 8/8/13 6:43 PM, Bin Liu wrote:
Hi All,
I would like to restrain the COM of a molecule, say a protein, in my
simulation. I found the pull code can do the job. However, I am not sure
about several parameters in the .mdp file.
For example, if I want to restrain the COM of the protein in only
first thing that I notice is that you are using PBC whereas Aqvist employed
a spherical boundary model. I also think that PME is not applicable for a
spherical boundary, so the reciprocal space contributions may be considered
as spurious if you want to reproduce the original results. Maybe you
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