2) Also I've found that there is more simple way to define restraines
based on the BONDS enty in the topology file. Could you provide me with the
more information about this simpler way ?
Simpler, but not a restraint to within a region. The manual section we are
discussing links you to the
On 16/03/2012 6:39 PM, James Starlight wrote:
2) Also I've found that there is more simple way to define
restraines based on the BONDS enty in the topology file. Could
you provide me with the more information about this simpler way ?
Simpler, but not a restraint to within a
Hi,
Thanks dear Justin for useful reply,
I have a system that is contained of protein-water-ions. I want to
calculate residue SAS of protein. In the first way, I select a group
consisting protein for calculation, and then this protein for output.
At the second way, I select the whole system
Hi Sara,
The bad performance you are seeing is most probably caused by the
combination of the new AMD Interlagos CPUs, compiler, operating
system and it is very likely the the old Gromacs version also
contributes.
In practice these new CPUs don't perform as well as expected, but that
is partly
The docs actually tells you:
Native GPU acceleration is supported with the verlet cut-off scheme
(not with the group scheme) with PME, reaction-field, and plain
cut-off electrostatics.
(http://www.gromacs.org/Documentation/Parallelization_and_acceleration#GPU_acceleration)
Use the cutoff-scheme
afsaneh maleki wrote:
Hi,
Thanks dear Justin for useful reply,
I have a system that is contained of protein-water-ions. I want to
calculate residue SAS of protein. In the first way, I select a group
consisting protein for calculation, and then this protein for output.
At the second way, I
Thanks a a lot to you and also to Szilárd for your feedback and
encouragement. I am very happy to see that this work is indeed useful
especially to developers.
We have no plans to make this into a 'proper' publication. I am not
sure how much interested the simulation community would be because,
Il 16/03/2012 01:38, Mark Abraham ha scritto:
On 16/03/2012 6:02 AM, Francesco Oteri wrote:
Dear gromacs users,
I am trying to simulate a protein (containing FeS cluster and a
complex metal active site) using virtual site.
I've to face a problem with LINCS. In particular, if I constrain only
Dear Gromacs Specialists,
I am very novice to Molecular Simulation study.
I am using GROMACS 4.5.4 version .
I completed some GROMACS tutorials , I not found any
tutorial on Simulated Annealing..
If Any one know the link please give me it..
I make my protocol to work on
On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote:
Hi Users:
I was trying to calculate the energy contribution of an specific ion in
my simulation. After extract a given frame from the simulation, I
recalculate
rama david wrote:
Dear Gromacs Specialists,
I am very novice to Molecular Simulation study.
I am using GROMACS 4.5.4 version .
I completed some GROMACS tutorials , I not found any
tutorial on Simulated Annealing..
If Any one know the link please give me it..
I make my
On 17/03/2012 12:39 AM, Anthony Cruz Balberdi wrote:
On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote:
Hi Users:
I was trying to calculate the energy
Thanks
On Fri, Mar 16, 2012 at 10:37 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 17/03/2012 12:39 AM, Anthony Cruz Balberdi wrote:
On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote:
Hi Users:
I was
You should absolutely publish this. it would be of great interest. You
can mitigate your chances of running into problems with the overview
by sending a version of the manuscript to the developers of each
software and asking them to provide a short paragraph, each of which
you could
Dear GROMACS users,
Obviously RMSD-based clustering is not the best approach to find frequently
visited conformations of flexible peptides. The other approach would be to
used backbone dihedral angles to cluster the frames (i.e. with g_dih).
There are also several articles in the literature
I am very novice to Molecular Simulation study.
I am using GROMACS 4.5.4 version .
I completed some GROMACS tutorials , I not found any
tutorial on Simulated Annealing..
If Any one know the link please give me it..
I make my protocol to work on simulated annealing as follow ...
(I am
Dear Gromacs user,
I am searching for the GROMOS (best would ffG53a5) forcefield parameters
of the rather rarely used amino acid AZIDOHOMOALANINE (C4 H8 N4 O2). The
residue looks like:
http://www.chembase.com/cbid_147480.htm
Every suggestion is very welcome since it can avoid doing the
Dear all,
I tried to install today Gromacs.
I downloaded gromacs 4.5.5, Cuda, FFTW3.
Installation of FFTW3 and Cuda went fine so far.
I managed to execute
sudo ./configure (in the gromacs untar folder).
sudo make
sudo make install
make links did not work and I cannot find gromcas. There is no
On 2012-03-16 20:19, bestenborstel wrote:
Dear all,
I tried to install today Gromacs.
I downloaded gromacs 4.5.5, Cuda, FFTW3.
Installation of FFTW3 and Cuda went fine so far.
I managed to execute
sudo ./configure (in the gromacs untar folder).
sudo make
sudo make install
Try running again
bestenborstel wrote:
Dear all,
I tried to install today Gromacs.
I downloaded gromacs 4.5.5, Cuda, FFTW3.
Installation of FFTW3 and Cuda went fine so far.
I managed to execute
sudo ./configure (in the gromacs untar folder).
sudo make
The above steps do not need to be executed with sudo.
Thank you for your quick reply.
'make links' produces:
Saturn:gromacs-4.5.5 gudrun$ make links
cd /usr/local/gromacs/bin programs=`ls` cd /usr/local/bin \
for i in $programs; do \
(test ! -f $i ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
done
/bin/sh: line 0:
On 2012-03-16 20:49, bestenborstel wrote:
Thank you for your quick reply.
'make links' produces:
Saturn:gromacs-4.5.5 gudrun$ make links
cd /usr/local/gromacs/bin programs=`ls` cd /usr/local/bin \
for i in $programs; do \
(test ! -f $i ln -s /usr/local/gromacs/bin/$i . ;
Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do
whatever I can :-)
What do you ask me please to do?
Am 16.03.2012 um 19:54 schrieb David van der Spoel:
On 2012-03-16 20:49, bestenborstel wrote:
Thank you for your quick reply.
'make links' produces:
On 2012-03-16 21:03, bestenborstel wrote:
Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do
whatever I can :-)
What do you ask me please to do?
sudo make install
and check on the screen where the stuff is copied to.
Am 16.03.2012 um 19:54 schrieb David van der
Did run sudo make install again, but before I executed configure with
prefix=/usr/local/gromacs and I did mkdir gromacs in /usr/local before
manually. Content in the gromacs folder: bin include lib share
Gromacs finished again with:
GROMACS is installed under /usr/local/gromacs.
Make
bestenborstel wrote:
Did run sudo make install again, but before I executed configure with
prefix=/usr/local/gromacs and I did mkdir gromacs in /usr/local before
manually. Content in the gromacs folder: bin include lib share
Gromacs finished again with:
GROMACS is installed under
Again 'sudo make links' gives:
cd /usr/local/gromacs/bin programs=`ls` cd /usr/local/bin \
for i in $programs; do \
(test ! -f $i ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
done
Is this good or bad, please?
g_luck is located for example now in
bestenborstel wrote:
Again 'sudo make links' gives:
cd /usr/local/gromacs/bin programs=`ls` cd /usr/local/bin \
for i in $programs; do \
(test ! -f $i ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
done
Is this good or bad, please?
In the absence of an
Hi,
I have a system that is contained of Protein-DOPC-SOL-Ions. I want to
calculate residue SAS of protein.The calculation group consists of all
the non-solvent atoms in the system (37 residue Protein+ 125 DOPC+14
ion),and then protein for output. Force files used for protein and
DOPC are ffg53a6
Dear All,
I meet the following error message for pdb2gmx. Please let me know how to solve
this problem.
Cheers,
Wholly Program pdb2gmx, VERSION 3.3.3
Source code file: futil.c, line: 542
Fatal error:
Library file FF.dat not found in current dir nor in default directories.
(You can set the
Dear All,
I use the following to neutralize the charge
genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn
8,
Then I do the following grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top
-o em.tpr.
However the feedback says there is no Na (sodium) moleculetype.
I am
On 17/03/2012 4:48 PM, Wholly Peach wrote:
Dear All,
I use the following to neutralize the charge
genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8,
Then I do the following grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr.
However the
Will you please tell me where can I find the ions.itp file?
I am looking forward to getting your reply.
Wholly
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Saturday, 17 March 2012 3:55 PM
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