Hi,
You can try the non-gromacs tool Concoord:
http://www.mpibpc.mpg.de/groups/de_groot/concoord/
http://151.100.52.62/pdf/046_amadei_proteins_1997.pdf
It was used e.g. in the CC/PBSA algorithm
http://ccpbsa.biologie.uni-erlangen.de/ccpbsa/
Hi everyone,
I ran my simulations with these parameters:
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb= 0.9
vdwtype = cut-off
rvdw= 1.2
Apparently, in Gromacs, when using vdwtype =
Dear all:
I was wondering did any one try to install the gromacs 4.5.X in your own
account of supercomputer cluster? I tried to do this, and I had some error
messages showed up.
First, for fftw installation, I did
./configure --enable-threads --enable-float --prefix=/home/chunxia/fftw
make
Oh, I did installation on supercomputer before. Because you are not root user,
in the step ./configure, maybe you should use ./configure
--prefix=/home/yourname/... to change the default installation directory.
Just my two cents. Hope it helps.
--hualin
Anna Marabotti wrote:
Dear gmx-users,
I have a protein with 5 different ligands. For each system I made 30ns
simulation and I calculated the lifetime of the H-bonds between protein
and ligand with the command:
g_hbond -f traj.xtc -s topol.tpr -hbm hbmap.xpm -hbn hbond.ndx -ac
hbac.xvg
Hi Mark,
I am not quite sure. While the details are different, I guess it is still
valid to compare some statistical properties, right? For example, I should
still be able to compare the average COM distance of these two ligands over
long trajectories, and make the conclusion that one is better
sorry, I wrote it wrong, actually I had added ./configure
--prefix=/home/yourname/... in it, but it showed the error message. so should
be like this:
First, for fftw installation, I did
./configure --enable-threads --enable-float --prefix=/home/chunxia/fftw
make
make install
everything is
Hi,
Based on the message it seem that autom4te (part of the autoconf
tools) can't write some temporary file to the standard temp location
/tmp. That would quite strange as if the temp directory is not there
$TMPDIR should be defined, but I suspect it's not, otherwise autom4te
would have picked it
Usually /tmp is writable for any user. It looks like this is not a case in
your system. Ask your system administrator.
dawei
On Tue, Oct 11, 2011 at 2:57 PM, Chunxia Gao chunxia@chem.gu.se wrote:
sorry, I wrote it wrong, actually I had added ./configure
--prefix=/home/yourname/... in
Hi Gregory,
I am not very familiar with the could computing offerings, but as far
as I know, in general they are not a very cheap solution when it comes
to relatively low usage (non massive enterprise use).
If you would need it only for you own research, you might be better
off with applying for
Igor Marques wrote:
chetan,
i'm not sure about the use of -sl option in g_order.
however, for the purpose you mentioned, i'd suggest you to:
create two different trajectories, using trjconv and an index file
grouping lipids closer to the protein and lipids away from the protein.
then, you
On 12/10/2011 3:48 AM, Yun Shi wrote:
Hi Mark,
I am not quite sure. While the details are different, I guess it is
still valid to compare some statistical properties, right? For
example, I should still be able to compare the average COM distance of
these two ligands over long trajectories,
On Wed, Oct 12, 2011 at 1:20 AM, Poojari, Chetan c.pooj...@fz-juelich.dewrote:
Hi,
I have protein completely inserted into lipid membrane and would like to
study order parameter around the protein as well as away from the protein.
For this I would like to slice my membrane into parts.
I
Hi, dear all,
I’m doing the simulation involved in protein and some surface.
I encounter this problem when trying to use implicit solvent model with
GMX4.5.3.
First, minimize. When doing this I got the result as below:
Step= 0, Dmax= 1.0e-02 nm, Epot= -1.91727e+06 Fmax= 6.19542e+06,
On 12/10/2011 3:59 PM, liaoxyi wrote:
Hi, dear all,
I'm doing the simulation involved in protein and some surface.
I encounter this problem when trying to use implicit solventmodel with
GMX4.5.3.
First, minimize. When doing this I got the result as below:
Step=0, Dmax= 1.0e-02 nm, Epot=
On 12/10/2011 2:22 AM, Nuno Azoia wrote:
Hello!
I found something very strange while making a CHCl3 box using gromacs-4.5.5.
A look the mailing list, the manual and some release notes for
gromacs-4.5 and I couldn't found the answer for my problem. It's
possible that I'm doing something wrong,
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