The sum of the two largest charge group radii (13.336) is larger
than rlist(1.2) - rvdw/rcoulomb i am getting this error while running
membrane simulations. please any one suggest how to rectify this error.
--
regards
M.SathishKumar
--
gmx-users mailing listgmx-users@gromacs.org
Probably, make your broken molecules whole before passing them to grompp.
Mark
On Tue, Oct 22, 2013 at 8:26 AM, Sathish Kumar sathishk...@gmail.comwrote:
The sum of the two largest charge group radii (13.336) is larger
than rlist(1.2) - rvdw/rcoulomb i am getting this error while running
Dear all users
I have simulated a protein with two chains (153 residues each) for
50ns(restarting crashed run 3 times) using a cubic box with each side as
11nm. After finding the closest distance between the periodic images, I
found that the closest distance becomes lesser than 1 after 23ns for
Hi Nidhi,
These are periodicity artifacts. Make sure that you remove jumps over PBC
from your trajectory by using trjconv -pbc nojump.
Cheers,
Tsjerk
On Tue, Oct 22, 2013 at 11:14 AM, Nidhi Katyal nidhikatyal1...@gmail.comwrote:
Dear all users
I have simulated a protein with two chains
Dear Sir,
I am doing fullerene interaction with DMPC , i downloaded
the gro file from the website mentioned in the tutorial. I was keep the
fullerene on the top of DMPC. But in the gro file already water is present.
If i removed that water molecules and adding new water
Thank you sir.
On Tue, Oct 22, 2013 at 2:48 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Nidhi,
These are periodicity artifacts. Make sure that you remove jumps over PBC
from your trajectory by using trjconv -pbc nojump.
Cheers,
Tsjerk
On Tue, Oct 22, 2013 at 11:14 AM, Nidhi
Hi Everyone,
I'm writing to let you guys know that we have developed a web-based tool MD
simulation tool for GROMACS. It is a software package primarily developed
for biological MD and offers a huge amount of possible options and settings
for tailoring the simulations. Seamlessly integrated with
Is there a link to the documentation? It's a little difficult to know
exactly what this supposed to be doing. Is it a GUI interface to
gromacs?
In general, it would be great to get these sort of extensions
coordinated with the main gromacs development tree, since otherwise
they would tend to
Dear all,
I have some doubt for the output force. What contributions do the output
forces in .trr file include? Certainly, the pair forces and bonded
interactions are included. However, if the external field (such as electric
field) is applied, is the external force included? In addition, if the
Hi Michael,
Sorry, if this is not the right place to post message of such. To answer
your question, it is a web-based GUI interface to GROMACS, which is a
perfect fit for those who are trying to learn MD or to run large scale
protein simulations on HPC.
Best Regards,
KevinFeng Chen, Ph.D.
On 10/22/13 9:15 AM, Sathish Kumar wrote:
Dear Sir,
I am doing fullerene interaction with DMPC , i downloaded
the gro file from the website mentioned in the tutorial. I was keep the
fullerene on the top of DMPC. But in the gro file already water is present.
If i removed
Hi Everyone,
I am having an awkward situation. I want to use g_density to get the
density profile of a lipid bilayer. At first glance, it looks like a
trivial task. But for my case, it's not because I have conflicting atom
names from two different molecules. I am using GROMOS 53a6. In DPPC
On 10/22/13 9:05 PM, Bin Liu wrote:
Hi Everyone,
I am having an awkward situation. I want to use g_density to get the
density profile of a lipid bilayer. At first glance, it looks like a
trivial task. But for my case, it's not because I have conflicting atom
names from two different
Hi!
It is strange but such combination works:
CC=icc CXX=icpc ~/cmake-2.8.12/bin/cmake ..
-DCMAKE_INSTALL_PREFIX=/ifs/apps/GROMACS-4.6.3 -DGMX_X11=OFF
-DGMX_MPI=ON -DGMX_FFT_LIBRARY=mkl -DGMX_GPU=ON cmake.log
It was a command that our cluster administrator was able to configure
GROMACS
I have some simulations of inserting a probe molecule into a bilayer. Some
molecules work fine. However, a certain class of molecules is taking an
absurdly long time to run the exact same simulation, even though I energy
minimized the molecules individually beforehand and there are no overlaps.
Hello,
I am running a NPT simulation for cyclopropylchloride(1) in
50%water(100)+50%ethanol(100) using opls force field parameter .
After equilibration box size increases from 20 A to 70 A.
I used the following mdp file.
; RUN CONTROL PARAMETERS =
integrator = sd
; start time and
It depending the time steps that u used or the molecule that u had is
big..Thats why ur EM take a long time..Is better take a long time
rather than quick but had a lot of errors..
On Wed, Oct 23, 2013 at 9:59 AM, Nimmy McNimmerson [via GROMACS]
ml-node+s5086n5011918...@n6.nabble.com wrote:
I
Hi,
We recently had a software upgrade in our cluster from gromacs 4.5.4. to
gromacs 4.6.3.. I need to continue an earlier simulation that had been run
in 4.5.4. using the .cpt, .tpr and .mdp.
Are there any issues with continuing these runs in 4.6.3.? Can I
concatenate these trajectories for
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