Hello:
I've got a question on energygrps options in .mdp file. This option is
usually used for establishing the groups for the energy output. I am
going to study the entropy changes of protein-ligand-SOL in a membrane
system, I am just wondering shall I specify each compoenent in
Hi all,
Just a quick question - and perhaps some wisdom from those with more experience.
I am trying to use metadynamics with gromacs to plot an energy landscape about
the rotation of two proteins. If I were to define my collective variables as
ThetaA and ThetaB, Theta being the rotation about
On 7/14/13 6:21 AM, Albert wrote:
Hello:
I've got a question on energygrps options in .mdp file. This option is usually
used for establishing the groups for the energy output. I am going to study the
entropy changes of protein-ligand-SOL in a membrane system, I am just wondering
shall I
Hello,
I am trying to run the qm-mm gas phase calculations for my system.
I am using following in md.mdp file.
title = cpeptide MD
cpp = /usr/bin/cpp
integrator = md
dt = 0.001; ps !
nsteps = 500 ; total 5 ps.
Hello,
How to compile Cygwin 4.6.3 for Windows using Cygwin ?
I did so:
tar xfz gromacs-4.6.tar.gz
cd gromacs-4.6
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON
(fftw 3.3 - install)
make
Error message
Thank you.
--
gmx-users mailing listgmx-users@gromacs.org
On 7/14/13 11:36 AM, Nilesh Dhumal wrote:
Hello,
I am trying to run the qm-mm gas phase calculations for my system.
I am using following in md.mdp file.
title = cpeptide MD
cpp = /usr/bin/cpp
integrator = md
dt = 0.001; ps !
On 7/14/13 1:04 PM, bh...@udsu.ru wrote:
Hello,
How to compile Cygwin 4.6.3 for Windows using Cygwin ?
I did so:
tar xfz gromacs-4.6.tar.gz
cd gromacs-4.6
The version 4.6 tarball will not give you version 4.6.3 :) Unless this is a
typo, make sure you're actually working with the
Error message, аfter the make:
In file included from
/cygdrive/d/1/gromacs-4.6.3/src/gmxlib/thread_mpi/atomic.c:38:0:
/cygdrive/d/1/gromacs-4.6.3/src/gmxlib/thread_mpi/impl.h:504:20: ошибка:
field «timer_init» has incomplete type
src/gmxlib/CMakeFiles/gmx.dir/build.make:8061: recipe for target
Hello dear users
I'm simulating gold nanoparticle interaction with protein. I want to change the
pH of system. What would need to be changed to simulate this system at pH 3.0?
thanks you
Fatemeh Ramezani
--
gmx-users mailing listgmx-users@gromacs.org
On 7/14/13 2:23 PM, fatemeh ramezani wrote:
Hello dear users
I'm simulating gold nanoparticle interaction with protein. I want to change the
pH of system. What would need to be changed to simulate this system at pH 3.0?
As is discussed frequently on this list (hint: check the archive for
Hi,
I'm want to run a MD simulation with a Phe-Phe-Phe-Phe-Gly cyclic peptide.
But I'm have problems generating the topology files. When I try to use the
strategy to generate a topology file for the linear GF
using
pdb2gmx -ff charmm27 -f pep.pdb -o pep.gro -ter -water spce
and choosing None
On 7/14/13 7:07 PM, jriedel wrote:
Hi,
I'm want to run a MD simulation with a Phe-Phe-Phe-Phe-Gly cyclic peptide.
But I'm have problems generating the topology files. When I try to use the
strategy to generate a topology file for the linear GF
using
pdb2gmx -ff charmm27 -f pep.pdb -o
Can anybody help me understand these better?
2013/7/10 lloyd riggs lloyd.ri...@gmx.ch
There vectors. Theres some good older papers explaining the whole thing
from Van Gunstern, Berendsen, and some other good ones from de Groot that
explain them well and includes combining them with other
any one please help me out with this problem?
2013/7/10 Ahmet yıldırım ahmedo...@gmail.com
Dear users,
I extracted separate extreme projections using g_anaeig. I have to make
pictures which show the difference. Can you help me, someone who makesthem
using pymolbefore
?
--
Ahmet
Hi,
How to get a snapshots in equal intervals of time (250ps) from production MD
trajectory. I'm using -sep , -t0, -timestep but output came only one .gro
file.
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View this message in context:
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On 7/14/13 9:03 PM, Rama wrote:
Hi,
How to get a snapshots in equal intervals of time (250ps) from production MD
trajectory. I'm using -sep , -t0, -timestep but output came only one .gro
file.
trjconv -skip -sep should work, but without exact command lines and the output
you received (as
Which papers have you read so far?
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
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When the only tool you own is a
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