Many thanks for your quick reply :)
On Tue, Apr 14, 2020 at 11:09 PM Justin Lemkul wrote:
>
>
> On 4/14/20 4:55 PM, Mohamed Abdelaal wrote:
> > Sorry for writing again in the same topic but I couldn't solve
> > the velocity problem.
> >
> > I am trying to reproduce a paper written by: Claire
Sorry for writing again in the same topic but I couldn't solve
the velocity problem.
I am trying to reproduce a paper written by: Claire Tonnel + , Martin
Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, Alpeshkumar
K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and
In Bob I'm _ bk no ññllkmjk mm lll look okk jul ki o ki olk by hmm j by by
he
On Tue, 14 Apr 2020, 6:33 pm Justin Lemkul, wrote:
>
>
> On 4/13/20 10:03 PM, Mohammad Madani wrote:
> > Dear all
> > Hi,
> > I have a basic question about the using the gromacs.
> > I want to use gmx cluster for
On 4/14/20 4:55 PM, Mohamed Abdelaal wrote:
Sorry for writing again in the same topic but I couldn't solve
the velocity problem.
I am trying to reproduce a paper written by: Claire Tonnel + , Martin
Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, Alpeshkumar
K. Malde, Paul L.
Many thanks Dr. Erik for your reply :)
On Tue, Apr 14, 2020 at 11:15 PM Eric Smoll wrote:
> No problem.
>
> Now it is clear what you are trying to do. The previous description of
> your goals did not make much physical sense. The initial velocities are
> such that all three dimensions are
Hi Gül,
You are absolutely correct! I just checked this with tau_t=10, and it
brought back the old behavior! Thank you so much for your suggestion!
Probabilities with tau_t=10, NH thermostat:
Repl 0 1 2 3 4 5 6 7 8 9 10 11 12
13 14 15 16 17 18
On 4/14/20 5:48 PM, Mohamed Abdelaal wrote:
Hello everybody,
I am simulating the evaporation process for different atoms on a graphene
sheet and the z-coordinate of each graphene carbon atom was restrained
(using position restrain).
The energy minimization was successfully done without any
My knowledge is a bit old.
Tpr files are binary so you cannot read them without a special tool. In
gromacs 2018, there was a tool that would spit out the contents of a tpr file
in a readable format. Execute
“gmx dump -h” to learn more.
Justin is correct. There is no tool or file that will
Hello all,
I am working with a rather large membrane bound protein. I was getting
an issue awhile ago where if the protein moved to the edge of the box
the box would elongate in the z direction. I fixed this in the short
term by setting my xy compressibility to 0 in my production mdp file
pcoupl
Gas phase simulations the inter-molecular interactions are smaller, and
intra-molecular interactions dominate. Therefore total energy will be
positive.
If it was filled with a solvent i.e. liquid phase, then inter-molecular
inteactions dominate and the total energy will be negative.
Catch ya,
Dear GROMACS users,
Since I have run the nvt and npt processes for the protein-ligand interaction,
I met the the warning messages below
Step 231785, time 463.57 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000176, max 0.003912 (between atoms 3035 and 3037)
bonds that
Hi Mohammed Madani,
Your command is missing the group as mentioned in the error message. While
correct for periodic error, you should ensure that you extract (that's if
your top/file has more than one groups) the appropriate group (not system)
from the production file (xtc) by using trjconv
Hi Jinyoung,
I guess that the LINCS WARNING you encountered maybe came from hiden errors in
the configuration of either protein or ligand OR more directly from the
ligand's topology. You need to carefully check the configuration of protein and
ligand, e.g. side chain goes through benzene ring.
Hi,
It was not gromacs 2020, but my fault and mixing up various tools
(grompp, mdrun) from 2019 and 2020 versions.
I am sorry.
Bests,
Tamas
On 4/14/20 4:44 PM, Tamas Hegedus wrote:
Hi,
There might be some bug(?) in gromacs 2020. I can not decide.
I just installed 2020.1 today using the
Hi,
There might be some bug(?) in gromacs 2020. I can not decide.
I just installed 2020.1 today using the same script (and libraries) what
I have used for gromacs 2019.
After energy minimization, in the nvt equilibration run, it stops:
Fatal error:
Step 0: The total potential energy is
On 4/13/20 10:03 PM, Mohammad Madani wrote:
Dear all
Hi,
I have a basic question about the using the gromacs.
I want to use gmx cluster for clustering. I use the cluster hpc.
When I run the this command:
gmx cluster -f *.trr -s *.gro -g *.log -clid *.xvg
I receive the error that I should
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