On 4/9/20 4:25 PM, Nadia Elghobashi-Meinhardt wrote:
Thank you, Justin.
I am still struggling with constraints.
I am trying to use "freezegrps" and "freezedim"
to run an NVT equilibration.
However, when I try to build the binary using my optimized structure, I get
either "Segmentation fault"
On 4/10/20 8:13 AM, Alex wrote:
Dear Justin,
Any comment please?
Sorry, haven't had power/network for a while due to some bad storms here.
GROMOS force fields are parametrized assuming all bonds are fixed, so
your constraints should be "all-bonds" not "h-bonds."
I would also suggest you
On 4/10/20 9:16 AM, Alex wrote:
Thank you for the response.
On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote:
On 4/10/20 8:13 AM, Alex wrote:
Dear Justin,
Any comment please?
Sorry, haven't had power/network for a while due to some bad storms here.
GROMOS force fields are
Dear Justin,
Any comment please?
Regards,
Alex
On Tue, Apr 7, 2020 at 5:38 PM Alex wrote:
> Thanks Justin for the response.
> Please find below the mdp file.
> The system is a thin film made out of a epoxy molecule, picture in be
> below link, with water on top and bottom of the film. I even
On 4/10/20 9:21 AM, FAISAL NABI wrote:
I have tried the same few days back but it didn't work. I have been using
gromacs 2018.1 earlier and then switched to 5.1.4 and it didn't work.
Switching between major versions that are years apart in their
development will not work, and GROMACS has
Hi Paul,
Thank you for your reply. In fact, there is the GMXPBSA tool but I still
have errors with that too when I run it on the examples provided in the
installation folder. I tried to seek some help but the developers aren't
responding.
Thank you anyway!
- Mariem
Le ven. 10 avr. 2020 à
Thank you for the response.
On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote:
>
>
> On 4/10/20 8:13 AM, Alex wrote:
> > Dear Justin,
> > Any comment please?
>
> Sorry, haven't had power/network for a while due to some bad storms here.
>
> GROMOS force fields are parametrized assuming all
I have tried the same few days back but it didn't work. I have been using
gromacs 2018.1 earlier and then switched to 5.1.4 and it didn't work.
On Fri, Apr 10, 2020, 6:43 PM Ashma Khan wrote:
> Dear all,
> I have run my simulation on gromacs 5.1.4 for 200ns but now I want to
> extend my
Dear all,
I have run my simulation on gromacs 5.1.4 for 200ns but now I want to
extend my simulation to 500ns with gromacs 5.1.2. Is it possible or will
there be problem during total simulation of 500ns in my systems. Please
give me suggestion regarding this.
--
Ashma Khan
Research Scholar
Hello,
there is no real supported way of doing this. You would need to
re-create the TPR in the version you want to use it in.
Can you use an external tool instead of g_mmpbsa that supports reading
the newer file format?
Cheers
Paul
On 09/04/2020 17:24, Mariem Ghoula wrote:
Hi,
I would
Hi All,
I have a coarse-grained simulation box with water and oil phases. Just
playing with the diffusion 'only on a single particle' (single martini
coarse bead) gave me different results when I use -rmcomm on trajectories
with and without -pbc nojump.
NOTE: selected only single bead
Same
Ah! am sorry, I figured out. Please ignore my mail.
I was using wrong group selection for rmcomm in the command line.
Sorry to all!
Dave
On Thu, Apr 9, 2020 at 11:26 PM Dave M wrote:
> Hi All,
>
> I have a coarse-grained simulation box with water and oil phases. Just
> playing with the
Hello All,
I am wondering if gromacs-2020 is buggy? or I am missing something?. In
gromacs-2020, for a certain setup, I got following warning,
WARNING: There are no atom pairs for dispersion correction
But, for same system, gromacs-2019 does not give warning. Apparently,
gromacs-2020 gives
Thank you, Justin.
I am still struggling with constraints.
I am trying to use "*freezegrps*" and "*freezedim*"
to run an NVT equilibration of a structure (successfully
geometry-optimized using freezegrps).
However, when I try to build the binary using my optimized structure, I get
either
On 4/10/20 12:15 PM, Elham Taghikhani wrote:
Hi
I want to simulate a protein which is bound covalently to a ligand. When I get
the gro file of the complex the bond between the amino acid and the ligand is
broken although I had modified the .rtp file before and it seems ok in a PDB
format.
Hi
I want to simulate a protein which is bound covalently to a ligand. When I get
the gro file of the complex the bond between the amino acid and the ligand is
broken although I had modified the .rtp file before and it seems ok in a PDB
format.
In the topology, I got this warning message :
Dear GROMACS developers,
I am performing classical MD simulations of a membrane protein system, using
GROMACS 2018.6 version. I have just noticed that after few nano seconds, the
box dimensions are changing. Meaning that the system shrinks along the z-axis,
for example dimensions are changing
On 4/10/20 11:04 AM, Yasaman KARAMI wrote:
Dear GROMACS developers,
I am performing classical MD simulations of a membrane protein system, using
GROMACS 2018.6 version. I have just noticed that after few nano seconds, the
box dimensions are changing. Meaning that the system shrinks along
Hello,
I guess the problem is about memory. You could strip the water and ions
first,
then process the striped trajectory.
All the best,
Qinghua
On 4/10/20 11:48 PM, Sadaf Rani wrote:
Dear Gromacs users
I am doing an analysis of protein-ligand MD simulation of 150ns. I am
trying to
On 4/10/20 4:17 PM, Alex wrote:
On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul wrote:
On 4/10/20 9:16 AM, Alex wrote:
Thank you for the response.
On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote:
On 4/10/20 8:13 AM, Alex wrote:
Dear Justin,
Any comment please?
Sorry, haven't had
Dear Gromacs users
I am doing an analysis of protein-ligand MD simulation of 150ns. I am
trying to calculate secondary structure as below:-
gmx do_dssp -f md_noPBC.xtc -s md.tpr -o ss.xpm -tu ns -dt 1
But I am getting segmentation fault error.
Reading file md.tpr, VERSION 2020-UNCHECKED (single
On 4/10/20 5:48 PM, Sadaf Rani wrote:
Dear Gromacs users
I am doing an analysis of protein-ligand MD simulation of 150ns. I am
trying to calculate secondary structure as below:-
gmx do_dssp -f md_noPBC.xtc -s md.tpr -o ss.xpm -tu ns -dt 1
But I am getting segmentation fault error.
Reading
Dear GROMACS users,
I read and followed Dr. Lemkul's tutorial on Free Energy Calculation on the
webpage, http://www.mdtutorials.com/gmx/free_energy/index.html
It is very helpful and easy to follow, but my ligand is protonated so the
atomic charges in the topol.top are non-zero.
The
On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul wrote:
>
>
> On 4/10/20 9:16 AM, Alex wrote:
> > Thank you for the response.
> >
> >
> > On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote:
> >
> >>
> >> On 4/10/20 8:13 AM, Alex wrote:
> >>> Dear Justin,
> >>> Any comment please?
> >> Sorry,
Dear Justin,
thank you for your answer.
As I noticed, there is a model of Drude oscillators (shells) used in GROMACS to
represent the polarization of atoms. However, there exists model of rigid rod
dipole moment which, instead of oscillating distance between the core nucleus
and the auxiliary
hi friends I generated a box of mixed gas with gmx insert-moleculesI ran an
energy minimizing. the potential energy is 4.05e+07 and maximum force is
1.25e+03.I used different algorithm likes cg and steep for minimization. what
do I have to do untill my system potential energy has negative
Dear Justin and Qinghua
I am using gromacs 2020 for analysis and dssp version on my system
is 2.2.1. Which version of dssp would be compatible with gromacs 2020?
Qinghua, I am already using the stripped trajectory. Any suggestions would
be appreciated.
Thanks.
Sadaf
--
Gromacs Users mailing
On 4/10/20 8:07 PM, Sadaf Rani wrote:
Dear Justin and Qinghua
I am using gromacs 2020 for analysis and dssp version on my system
is 2.2.1. Which version of dssp would be compatible with gromacs 2020?
Your version should be fine, but make sure the dssp binary works
properly on its own
On 4/10/20 9:03 PM, ferna...@hypernetlabs.io wrote:
Hi all!
Context
I'm trying to run simple gromacs example commands below
* gmx pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce
* gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter
-water spc
In a
Thank you Justin for your suggestion
As I run my simulation on supercomputer and there is availability of
gromacs-5.1.2 version not 5.1.4. Earlier it had 5.1.4 version but now it
has only 5.1.2 version.
--
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh
--
Gromacs Users mailing
On 4/10/20 9:20 PM, Ashma Khan wrote:
Thank you Justin for your suggestion
As I run my simulation on supercomputer and there is availability of
gromacs-5.1.2 version not 5.1.4. Earlier it had 5.1.4 version but now it
has only 5.1.2 version.
You can always install the version you want in
On 4/10/20 6:44 PM, Zuzana Benkova wrote:
Dear Justin,
thank you for your answer.
As I noticed, there is a model of Drude oscillators (shells) used in GROMACS to
represent the polarization of atoms. However, there exists model of rigid rod
dipole moment which, instead of oscillating
Hi all!
Context
I'm trying to run simple gromacs example commands below
* gmx pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce
* gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter
-water spc
In a Docker container with a Dockerfile (Dockerfile = instruction
Hi,
Based on what is in your system, what do you think the behavior should be?
A change reflects that one of the versions may be wrong, but not that the
new one is necessarily it.
Mark
On Fri, 10 Apr 2020 at 08:17, Parvez Mh wrote:
> Hello All,
>
> I am wondering if gromacs-2020 is buggy? or
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