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
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
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
http://www.r
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
function
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 r
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 t
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
> lipi
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
[…]
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 whitespace
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