Dear GMX users,
I would like to use multiple small molecules in the simulation system. The
topology files of the ligands were generated by swissparam. However, grompp
could not recognize the second ligand topology during the preparation of
system and gives following message:
'[ atomtypes
I've run protein adsorptions on PE, PEO, nylon and the like. The way I approach
such models is to first model the surface. Depending on if you want an
"extruded" polymer or a cast surface will define how you restrain it. For most
of my models - polymer strands of about 1000 atoms, and using
Thank you so much Dr. Lemkul.
Hadi
On Thu, Nov 7, 2019 at 2:04 PM Justin Lemkul wrote:
>
>
> On 11/7/19 12:26 PM, Patel, Lara Anne wrote:
> > Hi Hadi,
> >
> >
> > I have only gotten prints of "stepXXX.pdb" when something is going wrong
> with the simulation. That is not a printing option but
On 11/7/19 12:26 PM, Patel, Lara Anne wrote:
Hi Hadi,
I have only gotten prints of "stepXXX.pdb" when something is going wrong with
the simulation. That is not a printing option but rather supposed to help you in
diagnosing the problem.
This is indeed their intended purpose. If
Hi Hadi,
I have only gotten prints of "stepXXX.pdb" when something is going wrong with
the simulation. That is not a printing option but rather supposed to help you
in diagnosing the problem.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on
Hello gromacs users,
Can any body give me a reference page in gromacs manual for printing option
in energy minimization? I know for nvt other steps, but in energy
minimization it automatically prints a lot of "stepXXX.pdb" which are
unnecessary and I want to avoid that.
Thanks,
Hadi
--
Gromacs
Hello!
I am trying to simulate the adsorption of a certain peptide on a certain
polymer surface. For that, I did position restrain of polymer heavy atom and
position restrain of protein heavy atoms during the NVT and NPT equilibration
and also during energy minimization (EM).
The first
I would like to calculate rmsd of protein system, but there is much time
taking for trjcat of all simulated trajectories (.trr file) then generated
.xtc file by using -center -pbc mol flag. from this .xtc file i use to
calculate rms value by using flag g_rms -f .xtc -s .tpr -n .ndx -o .xvg I
want
Hi,
I would like to calculate the number of ligand molecules within 0.5 nm of a
particular amino acid in my protein. I came across the gmx trjorder command (as
shown below).
gmx trjorder -f Traj.gro -s Traj.tpr -n ProteinLIG.ndx -nshell nshell1.xvg -b
2 -e 4 -na 10 -r 0.5
I have 10
Hi John,
Thanks for the suggestion! Find a patch here that updates the mdp documentation
to clarify the issue you had with nsttcoupl:
https://gerrit.gromacs.org/c/gromacs/+/14157
Let me know if things are still unclear.
Best,
Christian
On 11/7/19 1:38 PM, John Whittaker wrote:
Hi
Hello Shradheya,
If you want to enforce dynamic load balancing you can use gmx mdrun -dlb yes instead of
the default "auto".
However, as I read from the output, your system was not balanced because it was not needed and the overhead of
re-distributing atoms might outperform the gain from it.
Hi Justin,
Thank you very much for the response. That's the conclusion I kept coming
to, but I'm happy to know it for sure now.
I'm not sure if others have been confused by this in the past, but it
would have saved me some trouble had I known that explicitly from the
beginning; any chance this
On 11/6/19 10:40 AM, John Whittaker wrote:
Hi all,
Please correct me if this is the wrong list for this particular question.
I have been messing around with the stochastic dynamics integrator in
version 5.1 (yes, it's relatively ancient, but I am testing some things
involving AdResS) and I
Respected Researchers,
How to balance the MD simulations? Below is the report.
*Dynamic load balancing report: DLB was off during the run due to low
measured imbalance. Average load imbalance: 1.4%. The balanceable part of
the MD step is 70%, load imbalance is computed from this. Part of the
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