On Jun 23, 2011, at 5:07 AM, Anja Kuhnhold wrote:
I'm simulating a bead-spring polymer model (1600 chains and 10 beads per
chain in a 26.6^3 box with pbc) with LJ and FENE potentials.
I calculate the mean-square-displacement for different temperatures. For
T=0.46 (in LJ units) I expected to
Hello all,
I noticed significant changes in my simulation results between running gromacs
4.5.1 with the included amber-gs-s force field and gromacs 4.0.7 with Eric
Sorin's amber ports. I eventually figured out that the parameter files in the
amberGS.ff directory are identical (up to
I am getting the following warning message from g_rama, even for a simple
system like a blocked Alanine dipeptide:
$ g_rama -s test.tpr -f traj.xtc
[…]
Reading file test.tpr, VERSION 4.5.1 (single precision)
Found 1 phi-psi combinations
Dihedral around 6,8 not found in topology. Using mult=3
[…]
On Nov 11, 2010, at 6:35 PM, George Khelashvili wrote:
I am relatively new to Martini force fields and the fact that masses of all
the coarse grained beads are set to a same value (72amu) somewhat bothers me.
I was wondering what influence may this have on the process of spontaneous
lipid
On Nov 22, 2010, at 3:09 AM, mohsen ramezanpour wrote:
I am searching for a tutorial for learning how to do protein folding with
Gromacs.
Do any one know such tutorials?
Not exactly a tutorial, but you can find Gromacs input files, as well as
several hundreds of microseconds worth of MD
On Nov 29, 2010, at 5:58 PM, sreelakshmi ramesh wrote:
Basically i have been using a sampling method called FFS to calculate the
rate constant for folding of a protein .The umbrella sampling done on the
system shows there is high barrier between the reac an prod states The phase
spece
On Nov 29, 2010, at 8:52 PM, sreelakshmi ramesh wrote:
Lutz ya you are true but as you said how can i change the velocity for a
config every move as in TPS?since i have not done tps i have no idea abt this.
You can't, neither for TPS nor for FFS. I don't think Gromacs provides this
I ran into some issues with the Gromacs web site:
1. I tried to register an account on the bug tracker
(http://redmine.gromacs.org/account/register). Upon entering my
information, I get the odd error message Email notifications is not
included in the list. Perhaps this is related to
On Apr 6, 2011, at 9:08 PM, Qin Qiao wrote:
the command I use:
g++ test.cpp -o test -I/usr/local/gromacs/include/gromacs
-L/usr/local/gromacs/lib -lgmx
./test
Error:
./test: error while loading shared libraries: libgmx.so.6: cannot open shared
object file: No such file or
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