Dear all,
My system consists of a three chains of protein: PROA, PROB and PROCLIG
(with ligand).
Minimization is running properly without any error.
Parameters used are:
title = Minimization ; Title of run
define = -DPOSRES
; Parameters describing what to do, when to stop and what to
Dear Gromacs Users,
I ran the MD simulation of Membrane environment of protein at 100ns. I
would like to analysis of clustering methods.
I am planning to generate 'rmsd-matrix.xpm' and run 'gmx cluster' job but i
don't know which group select both for cluster analysis. could you guide
me, how to
Dear gromacs users,
I want to calculate Orientational tetrahedral order parameter of water. The
output of gmx_hydorder is confusing. can I use gmx_order instead?
Thanks,
Subhadip Basu
Ph.D Student
Materials Research Centre
Indian Institute of Science
Bangalore 12
Contact no. +918277396508
--
Thank you for your suggestion Alessandra Villa
I have applied all types of pbc conditions but my one peptide is diffusing
away from another peptide in case of dimer after half of the simulation
time and rmsd is coming out 100 Angstrom after that time which is very
high. Please suggest me what
You welcome. Also there is detail information on the pbc correction on
gromacs page, kindly see that.
Bhupendra
On Fri, Jan 17, 2020, 4:02 AM Rabeta Yeasmin
wrote:
> Hi,
>
> I have solved the issue. I had problem in pbc correction step. It is good
> to follow some steps in order to get a good
Dear users,
If H-D-A angle is 30 degrees (for a case D-H distance is 1.0 A and D-A
distance is 3.3 A)
then the angle D-H-A is 138.3915 degrees.
D-A distance: 3.3 Angstroms and H-D-A angle: 30 degrees
are generous criteria to identify most hydrogen bonds.
It seems many people use them too.
On
are at
https://github.com/lanselibai/gromacs-20200116
The MD is run on our HPC cluster. So I personally could not compile it. Is
there still some way to get equivalent performance for the Version 2019?
Try assigning the same number of PP and PME ranks in each run (30/6 in
5.1.1 and 27/9
On 1/16/20 10:07 AM, András Ferenc WACHA wrote:
Dear Justin,
thank you. Am I doing something wrong or is this a bug in Gromacs? Do
you have a suggestion how to make this work? Should I rename the
terminal patches or should I put everything under one basename
(sacrificing cleanliness and
Hi,
I have solved the issue. I had problem in pbc correction step. It is good
to follow some steps in order to get a good result. What I have used is
-First made the molecules as whole to remove stretching in the structures
(protein, membrane) due to pbc effect.
*gmx trjconv -s
Dear users,
I might need an help with gmx trjconv.
I have a system with a lysine + a micelle attached on it and I have to
analyse the radial spherical distribution on the micelle.
The idea is to center the micelle and to work on it.
I used the command "gmx trjconv - cluster" to get a
-20200116
The MD is run on our HPC cluster. So I personally could not compile it. Is
there still some way to get equivalent performance for the Version 2019?
--Original--
From:"ZHANG Cheng"<272699...@qq.com;
Date:Thu, Jan 16, 2020 07:58 AM
To:
I will look into this and get back to you again. But meanwhile just try
using .tpr file instead of.gro file in your pbc correction step.
Thanks
Bhupendra
On Thu, Jan 16, 2020, 10:07 PM Rabeta Yeasmin
wrote:
> Hi Bhupendra,
>
> Thanks for your reply. The RMSD is actually 3.5nm means 35A, which
Hi Bhupendra,
Thanks for your reply. The RMSD is actually 3.5nm means 35A, which seems
very large compared to the RMSD of that protein in all-atom simulation
which is mostly between 5-6A. I have checked the trajectory as you
suggested, My system is a dimer protein inside a lipid bilayer and it
The ambiguity in the gromacs 2020 note made me concerned, as it was
not clear to me whether my system (DNA+small molecule) fills in the
category where artifacts are caused. The gromacs note could have been
a bit more helpful by referencing specific publications so that we can
educate
Okay, thanks, I created a redmine request: #3304
On Wed, Jan 15, 2020 at 11:23 PM Michael Shirts wrote:
> The simulated tempering options haven't been as well tested as the
> hamiltonian expanded ensemble version. The weights SHOULD be showing up in
> the column that says -nan, but clearly
Dear Justin,
thank you. Am I doing something wrong or is this a bug in Gromacs? Do
you have a suggestion how to make this work? Should I rename the
terminal patches or should I put everything under one basename
(sacrificing cleanliness and maintainability)?
Kind regards,
Andras
On 1/16/20 2:47
Hi,
You can patch Gromacs with Plumed and use hrex:
* generate a full .top file of your system (with -pp in the grompp command)
* open your .top and add "_" in the second column (type) of each atom you
want to apply REST2 in the [ atoms ] section of the moleculetype
* use the command "plumed
On 1/16/20 8:44 AM, András Ferenc WACHA wrote:
Sorry, now replying to the whole list:
Dear Justin,
I have obtained the base force field from the website of the MacKerell
Lab
(http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2017.ff.tgz).
I have checked
Sorry, now replying to the whole list:
Dear Justin,
I have obtained the base force field from the website of the MacKerell
Lab
(http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2017.ff.tgz).
I have checked and the merged.n.tdb file is the same in my version
On 1/16/20 8:04 AM, András Ferenc WACHA wrote:
Dear fellow Gromacs users,
I have developed an extended version of the CHARMM36m force field for
beta-amino acids (https://charmm-betaff.readthedocs.io,
https://gitlab.com/awacha/charmm-beta.ff). For beta-amino acids I found
pdb2gmx works well.
Dear fellow Gromacs users,
I have developed an extended version of the CHARMM36m force field for
beta-amino acids (https://charmm-betaff.readthedocs.io,
https://gitlab.com/awacha/charmm-beta.ff). For beta-amino acids I found
pdb2gmx works well. However, if I try to use it for natural peptides and
On 1/16/20 5:17 AM, Alessandra Villa wrote:
Hi,
On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris
wrote:
dear all,
I installed gromacs 2020 and I now get the following message during
equilibration:
NOTE 1 [file nvt.mdp]:
Removing center of mass motion in the presence of position
On 1/15/20 10:05 PM, Myunggi Yi wrote:
Dear Dr. Justin Lemkul,
Can you explain why the D-H-A is 150?
If H-D-A is 30, then D-H-A should be smaller than 150 degrees.
Since the sum of interior angles of a triangle should be 180 degrees...
See the following triangle.
H
D
Dear colleagues,
we have an open Post-doc position for those interested in the
biomolecular simulations, and in particular ligand-transport mechanisms
in enzymatic action, and/or method developement. The position is available
asap, - for details please see:
Many thanks for your reply. These links are really helpful.
On Thu, 16 Jan 2020 at 14:51, Alessandra Villa <
alessandra.villa.bio...@gmail.com> wrote:
> Hi,
>
> my suggestion is to move to Verlet scheme -
> (
> http://manual.gromacs.org/documentation/2019/user-guide/cutoff-schemes.html
> )
> See
Hi,
my suggestion is to follow the indication that you got from the error
See the mdrun " option -rdd, for pairs and tabulated bonds also see option
-ddcheck"
Best regards
Alessandra
On Wed, Jan 15, 2020 at 12:33 AM Sadaf Rani wrote:
> Dear Gromacs users
> I am facing this error during free
Hi,
On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris
wrote:
> dear all,
>
> I installed gromacs 2020 and I now get the following message during
> equilibration:
>
> NOTE 1 [file nvt.mdp]:
>
> Removing center of mass motion in the presence of position
> restraints might cause artifacts
>
>
Hi,
On Tue, Jan 14, 2020 at 7:41 PM Travis Meyer
wrote:
> Hello all,
>
> I am a brand new MD/GROMACS user, and I have been trying to learn how to
> use GROMACS for coarse-grained simulations using the MARTINI forcefield. I
> was going through a tutorial on coarse-graining from the MARTINI
Hi,
I suggest to visualize your trajectory. Maybe one of the peptide is
diffusing away from the other.
Or the one peptide is jumping in and out or moving out the box.
If it is the case, here you found some trjconv workflow
That tells you what your CPU is capable of. We need to know whether cmake
has found the compiler that can issue the instructions. Follow the
suggestions Roland and I have made.
Mark
On Wed, 15 Jan 2020 at 10:45, Shlomit Afgin
wrote:
>
>
> I ran:
>
> cat /proc/cpuinfo | grep -i avx512
>
>
>
>
Hi,
my suggestion is to move to Verlet scheme -
(http://manual.gromacs.org/documentation/2019/user-guide/cutoff-schemes.html
)
See also for
http://manual.gromacs.org/documentation/2020/release-notes/2019/major/deprecated-functionality.html#functionality-deprecated-in-gromacs-2019
You could
Hi,
gmx genconf is not generating xtc files. -trj option allows to use the
trj frames to expand gro/pdb files.
For example using -nbox 2 2 2 the first 8 frames of the trj file will be
use to build the new gro/pdb file.
A possible alternative is to use If you want to visualize you xtc-file
Hi Alex,
It's not possible with genconf. genconf only ever outputs a single
structure. If you provide a trajectory, each frame in the trajectory is
matched with a grid position that is then output as a single structure.
If you're looking into this for the sake of visualisation, tools like
33 matches
Mail list logo
