Hi Maryam,
If I am not wrong, VOTCA-CSG (http://www.votca.org) is the package that
might help you. It parameterizes course-grained potentials based on
structural properties of the system using different approaches including
the iterative Boltzman Inversion (iBI). All the GROMACS files can be
I am not sure if it is for martini or not but one that may be adapted (from
what I can tell) is VOTCA .
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Maryam Sadeghi
Sent: Friday, November 1, 2019 7:32 PM
To: gmx-us...@gromacs.org
Subject:
Dear All,
I was wondering if there are any codes in GROMACS for doing Iterative
Boltzman Inversion to reproduce the target pair distribution functions for
a MARTINI coarse grained structure given by atomistic simulations?
Best
Maryam
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Hi, All
There are four columns from the output of gmx h2order, mux, muy, myz,
cosine with normal.
What are they? Can anyone further explain?
Decai Yu
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Hello Everyone,
I am currently running a CG MARTINI simulation on a bilayer of POPC Lipid
in Water. I also have a single vitamin E in the mixture aswell (inside of
the POPC bilayer). I am trying to perform umbrella sampling by pulling the
vitamin E and measuring it's binding energy to POPC. I am
Den 2019-11-01 kl. 17:07, skrev Mijiddorj B:
I would like to simulate a system which contains a silicon oxide surface
and a polymer. Is it possible to simulate in gromacs?
I thought that GROMOS force field could be applied in this purpose. Is it
right? I am not sure.
If you have a potential
I would like to simulate a system which contains a silicon oxide surface
and a polymer. Is it possible to simulate in gromacs?
I thought that GROMOS force field could be applied in this purpose. Is it
right? I am not sure.
Also, is it possible to use InterfaceFF and Charmm force fields for this
Hi GROMACS users,
The second beta release of GROMACS 2020 is now out and available!
As before, we are making the testing versions available for you to be
able to get feedback
on how well things are working, and what could be improved or if there
are any bugs
in the code we have missed
*GROMACS compiled and installed in the shared folder using:-*
cmake .. -DCMAKE_INSTALL_PREFIX=/home/drug/Desktop/share/test
-DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON
-DCMAKE_BUILD_TYPE=Release -DGMX_MPI=ON -DGMX_BUILD_UNITTESTS=ON
-DCMAKE_C_COMPILER=mpicc
during rdf calculation i used flag gmx rdf -n .ndx -o .xvg -f .xtc -s .tpr
it prompt Specify a selection for option 'ref' then i had given one one
reference group 17 then it appear Selection '17' parsed then any number of
selections for option 'sel' again it apper Selection '19' parsed .how can i
thank you sir
On Thu, Oct 31, 2019 at 3:37 PM Justin Lemkul wrote:
>
>
> On 10/31/19 6:02 AM, shakuntala dhurua wrote:
> > thank you sir, by this gmx trjconv -center -pbc mol the two chains are
> > coming closer but still rmsd result is high and fluctuating highly while
> > taking two chain at
On 11/1/19 7:40 AM, Shradheya R.R. Gupta wrote:
Respected Researchers,
I am trying to run GROMACS in parallel. So I have established connection
using ssh, nfs and openmpi.
The connection is working fine as I have run Autodock Vina-MPI and other
test files.
I have installed the GROMACS in
Respected Researchers,
I am trying to run GROMACS in parallel. So I have established connection
using ssh, nfs and openmpi.
The connection is working fine as I have run Autodock Vina-MPI and other
test files.
I have installed the GROMACS in the mounted directory which is shared by
all the
Hi
You can follow the link below
http://www.mdtutorials.com/gmx/umbrella/index.html
On Fri, Nov 1, 2019 at 10:40 AM Rakesh Mishra wrote:
> Dear Justin
>
> If we have simple duplex of DNA initially and than we have separated
> both the strand by constant velocity stretching. Hence now we have
Hello Neena,
The outline you give appears reasonable for exploring peptide conformations. It is very hard to judge appropriateness
though without knowing what you are trying to learn from your system.
The unspecified position restraints might defeat the purpose of the simulated annealing if
Hello Saranya,
Now again with readable formatting. Also note that it is very useful to people
on gmx-useres to specify the subject when writing emails, because it makes it
easier to search, reply, and handle multiple discussion threads.
This error means that during the nvt equilibrium high
Hello Saranya,This error means that during the nvt equilibrium high forces
occurred that made it impossible to resolve the bond constraints. The very high
forces occurred most likely are due to some high tension in the system. As
indicated in the error message you can. Reduce the time step of
Hello everyone,
while running nvt equilibration i am getting the error as:
Step 12, time 0.024 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 92522.640625 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current,
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