Hello,
I am trying to understand, how Gromacs calculates the virial for periodic
systems. According to
Eq. B.11 in the Gromacs manual, this should be a function of the total forces
of the particles.
However, I don't understand, how delta_i is being calculated.
As far as I can see it is
Dear Gromacs users,
I am interested in simulation of lipid bilayers with Gromos96 53a6.
As I understood this force field has been parametrized with reaction field
instead of pme.
Based on literatures, I have the following .mdp parameters:
But I am not sure of those as my system has lots of LINCS
I do not see much connection between bond constraints and treatment of
electrostatics beyond the cut-off distance.
There is also an epsilon_r keyword. I would investigate what exactly
it means and whether it is used in the reaction field procedure.
The all-bonds contraint often results in
I have a strong belief that an error bar for such numbers exceed the
diffusion coefficient values.
Newer gromacs versions (or is it just because of a double-precision
compilation?) output more digits. I do want to hope these digits are
meaningful
If I got this situation, I would report
Dear Gromacs users,
We ran a simulation of an AOT reverse micelle in isooctane solvent. We
followed instructions
http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering . For
clustering we selected the group that contains AOT and for output we
selected the entire system. The reverse
Yes, for some calculations the error bar values did exceed the diffusion
coefficient values.
I am using the double-precision version of gromacs. But then again the
question is whether to consider the value displayed on the terminal screen
or the one displayed in the .xvg file.
On Tue, Jul 21,
On 7/20/15 10:15 AM, minky son wrote:
Thank you for kind answer,
After I ran the simulation, the all values resulted from Free energy
calculation in Justin tutorial were almost same.
But I have difficulty in drawing histogram using xmgrace. Whenever I draw
the histogram, it showed totally
On 21/07/15 17:32, Julius Schulz wrote:
Hello,
I am trying to understand, how Gromacs calculates the virial for periodic
systems. According to
Eq. B.11 in the Gromacs manual, this should be a function of the total forces
of the particles.
However, I don't understand, how delta_i is being
Hi Joao,
Thanks for comment, I am using 4.6.7 version.
On Tue, Jul 21, 2015 at 12:09 PM, João M. Damas jmda...@itqb.unl.pt wrote:
I have not looked thoroughly to your parameters, but which version of
GROMACS are you using? Any version from 4.5.X onwards is known to be
problematic with
Am 21.07.2015 um 20:44 schrieb David van der Spoel sp...@xray.bmc.uu.se:
On 21/07/15 17:32, Julius Schulz wrote:
Hello,
I am trying to understand, how Gromacs calculates the virial for periodic
systems. According to
Eq. B.11 in the Gromacs manual, this should be a function of the total
Hi Chaban,
Me too, but I do not know why starting with the same initial structures and
also starting from equilibrated structures again cause LINCS problems in
one not in the other one.
I have tried lincs-iter and lincs-order and also lincs allowable angle
deviations but LINCS error still exist.
Maybe indeed downgrade to an earlier version.
I, for sure, successfully used reaction field with gromacs 3-3-3
(imagine when it was).
Professor Vitaly V. Chaban
On Tue, Jul 21, 2015 at 4:49 PM, Mohsen Ramezanpour
ramezanpour.moh...@gmail.com wrote:
Hi Chaban,
Me too, but I do not know why
Hi Szilárd ,
The test case worked after I added the flags you recommended, though the
speed was not as high as I had hoped - equivalent to about 6 CPU cores -
I guess my GPU is not so hot.
Below is the output from mdrun -version. Please let me know if you
see things that might be optimized
The general advice to use trjconv with every keyword independently.
In certain cases, its behavior is fairly bizarre if one uses all
keywords at the same time. Probably, order of called procedures in the
code matters...
Professor Vitaly V. Chaban
On Tue, Jul 21, 2015 at 3:08 PM, Tyler
I looked at the first link, it was a useful discussion.
Now, I am trying suggestions with rlist/r(columb/vdw)=(1.4/1.4) and
everything is working properly till now.
It seems the problem was the twin-range + RF with this version of Gromacs
as has been discussed and you mentioned already.
I am
I really think you may be losing time with LINCS parameters. Look at these
links too:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/088108.html
http://redmine.gromacs.org/issues/1400
You use a twin-range, i.e. a rlist/r(coulomb/vdw) of 0.8/1.4, so I really
think that
Hi,
Actually you are right. The chol.xvg file shows a value of 0.000903331 and
NOT 0.000903331*1e-5. I initially thought that the .xvg file purposely
doesn't show the 1e-5 value.
But still 0.000903331 is different from 0.0007417 which is displayed on the
terminal screen.
On Tue, Jul 21, 2015 at
Hi,
With heavyh you redistribute the mass of the system, making hydrogen
heavy by taking mass from the attached atom. In that way the total mass
remains unchanged, but you can use a bigger time step (I think it's
meant for 4fs).
Felipe
On 21/07/15 07:28, Sana Saeed wrote:
what is the main
It's not clear from your question what you exactly want to calculate, but
g_sgangle (Gromacs 4.6 and earlier) and gmx gangle (Gromacs 5.0+) can
calculate angles between vectors. g_sgangle has somewhat limited
capabilities, but if you just want two vectors with endpoints at certain
atoms, it should
Dear All,
I am trying to install gromacs 5.0.5 in cygwin. I am getting linking errors
to fftw. although i have added the path in my bashrc file. can someone help
.
the errors:
../libtool: line 6002: cd: home/ashmer/fftw-3.3.4/fftw-3.3.4/lib: No such
file or directory
libtool: link:
Gromacs has OPLSAA force field. You can use pdb2gmx command.
Also you can use topolbuild software. If you google it, you can easily find
how to use it.
On Tue, Jul 21, 2015 at 2:38 PM, Daniele Veclani danielevecl...@gmail.com
wrote:
Dear users
I'm trying to create a topology file for a
thanks for
On Tuesday, July 21, 2015 11:28 AM, Felipe Merino
felipe.mer...@mpi-dortmund.mpg.de wrote:
Hi,
With heavyh you redistribute the mass of the system, making hydrogen
heavy by taking mass from the attached atom. In that way the total mass
remains unchanged, but you can
Dear users
I'm trying to create a topology file for a molecule to oplsaa force fields
How can I do this?
I have read that I can do this with the program MKTOP but I can not use it.
Is there a tutorial for this program?
Best regards
Daniele.
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Hi,
Libkernel is not a thing in 5.0.5, so you ate somehow getting interference
from an old install of gromacs. E.g. clean that out.
Mark
On Tue, 21 Jul 2015 09:45 Ayesha Fatima ayeshafatima...@gmail.com wrote:
Dear All,
I am trying to install gromacs 5.0.5 in cygwin. I am getting linking
Dear Atsutoshi,
Very thanks for your reply. I run repulsive/nonrepulsive potential
simulations for a system contains (Di-peptide + 2Ligand) for 5ns as
suggestions and, compared final results by VMD. I don't think that there is
really difference between two simulation, ligands are aggregated in
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