Dear GMX users,
I have a question regarding GMX RDF and I apologize if my question is too basic.
My trajectory consists of a dimer inserted in a membrane with an explicit
water/ion environment. I would like to compute the distribution of the center
of mass of lipid molecules to the surface of
Dear Gmx users,
I've been using Gromacs to perform Principal Component Analysis on my
trajectories.
1- With gmx anaeig, we can plot a 2d projection of a trajectory on eigenvectors
1 and 2 (for example). I would like to know if there is a way to obtain the
same plot but where the points are
Thanks a lot, Kevin for your comments and help.
Zeineb
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Dear Kevin,
Thank you for your reply.
I did 2 tests:
1- I wanted to see in details when the system crashes and which atoms are
involved so I restarted the simulation from the checkpoint but using a new mdp
file. The only parameter that I changed was nstxout-compressed = 1. In this
case, the
Dear GMX users,
I am running a Coarse-Grained simulation using Martini Force Field. My system
consists of a Protein inserted in a lipid bilayer containing POPC, POPE, and
CHOL molecules, in the presence of Water and ions.
I followed the conventional steps to prepare my system for the
Finally, I visualized the data in the output file of -otilt (tilt_TMC1CA.xvg)
using xmgrace with the command: xmgrace -nxy tilt_TMC1CA.xvg
I read again the documentation of gmx helixorient and if I understood well, the
values of the tilt angle of the helix axis to the membrane plan are
Dear GMX users,
I would like to calculate the angle of a transmembrane helix long axis with
respect to the membrane normal and see how this angle fluctuates during the
simulation.
In the forums, people were suggesting to use gmx helixorient. I used it with
the following command:
gmx
Dear all,
Thank you for your suggestions and help.
@Quyen, I checked the energies, box fluctuations and pressure deviations and
everything seem correct: Energies (potential, kinetic and total) were stable
during the simulation and the average of the pressure was 1.04 bar.
@ Peter, I
Dear GMX users,
I'm running a coarse-grained simulation of a homo-dimer in a membrane composed
of POPC, POPE, and CHOL (31%, 41%, 28% respectively), using MARTINI force field
and GROMACS software.
I followed the usual steps with 1ns minimization, 50 ns NVT equilibration
followed by 50ns NPT
Dear Justin,
Again, thank you very much for your fast reply, which is very clear. However,
I'm having difficulties to understand how the tools that I'll use will not
depend on the force field parameters.
For example, I'll use gmx_order to compute the order parameter per atom for
carbon
Dear Justin,
Thank you very much for your help and clarifications.
I have a question please:
I used OPLS-3 force field when running my simulations with Desmond, which is
absent in GROMACS 5.1.3
In order to generate the topology (protein and POPC), I guess I have to work
with the same force
Dear gmx users,
I'm running simulations on membrane proteins (POPC) using Desmond software and
I would like to use GROMACS tools to analyze certain parameters related to the
membrane. Exemple:
- Deuterium order parameters of the acyl chains
- Density of the membrane environment
- Area per lipid
Thank you very much Justin,
I'll add the [bonds] parameters and I'll let you know.
Regards.
Zeineb
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Dear gmx users,
I'm working on a Hemprotein (homodimer) and I'm having some troubles with
pdb2gmx in order to recognize the Fe-S bond (between the hem and a residue of
my protein):
In my pdb2gmx command, I'm using chainsep option in a way that the HEM and the
protein belongs to the same
Dear Mark,
Thank you very much for your help.
I checked the .itp file of my new parametrized molecule (THF) generated by
pdb2gmx and it is not completed (only [atoms] entry, there is no [bonds],
[angles] or [dihedrals] entries. Effectively, pdb2gmx failed to generate the
topology of the
These VMD warnings are normal I guess, I had them when I opened another PDB
file (that contain the THF and it was correctly displayed!).
Zeineb
When I verified the output of VMD after opening the file I had these warnings:
Warning) Detected a mismatch between CUDA runtime and GPU driver
Warning) Check to make sure that GPU drivers are up to date.
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension:
I verified the names in the .gro files: all the names are OK!
I also verified a C=C bond distance (within an aromatic cycle) and it is = 3.67
(I took a PDB file used to generate this model and which contain the THF, the
distance between the same atoms were 1,43!!)
Zeineb
Dear Mark,
Thank you for your orientation. I looked in Google and based on what you
advised me, I prepared the following mdp file
integrator = steep
nsteps = 1000
emtol = 1000.0
emstep = 0.01
energygrps= system
pbc = no
nstlist = 0
ns-type = simple
rlist = 0
Dear Mark,
Thank you very much for your answer.
I'm trying to minimize my protein in vacuo but I'm havig problem to undrstand
the concept of "in vacuo" so I'm enable to construct an mdp file and I can't
found valid examples in forums and internet. Could you help me with that please?
Also,
Dear gmx users,
I'm having problems during my energy minimisation step, I tried different
options in the mdp file but I'm enable to fix the problem, I'm hoping that you
can help me with this.
My system is a dimer that contain HEM, cofactor (Tetrahydrofolate, THF) and
arginin (substrate).
@Justin,
Thank you very much for your help, I finally fixed the problem but I'm having
another one with grompp (which was expected): The error that I get is:
ERROR 7 [file topol.top, line 41571]:
No default Proper Dih. types
Fatal error:
There were 13 errors in input file(s)
I think that
I'm looking to generate the topology of a HEM protein , I choose CHARMM as a
force field. At the begining, when I run pdb2gmx I had this error about missing
hydrogen's:
WARNING:
atom HA is missing in residue HEM 473 in the pdb file
You
might need to add atom HA to the hydrogen database
Dear all,
I'm desperetly looking for help to generate the topology of my hem protein.
I'm using CHARMM as a force field and apparently PDB2gmx assigns
dihedrals that should not exist and it's complicated to verify everything.
Justin suggested using
@ Justin
Dear Justin,
Thank you very much for the links. I'll read the articles and see how I can fix
my topology file!
Zeineb.
@ Justin
Dear Justin,
Thank you very much for the website.
I tried to generate my topology from the website. After many problems in my
input file, it finally generated the .str file with no error/warnings found but
unfortunately some penalties were not good at all (> 50 and between 10
@ Justin
Dear Justin,
Thank you very much for your orientation and help.
I visited CHARMM-GUI website and I found interesting tutorials for my
HEM-protein but before going further I would like to know if it's feasible to
use CHARMM GUI for my Hem-Protein and include after my substrate
Dear gmx users,
I'm working on simulating a homodimer with its cofactors (hem, THG) and its
substrate with GROMACS.
Since my system is complex, I decided to start first with a monomere taking
only protein residues and the hem group.
When I run pdb2gmx, using CHARMM27 FF, I had this error:
Dear gmx users,
I'm working on simulating a homodimer with two cofactors (hem and
tetrahydrofolat) and its substrate.
My system is complex so I decided to build my topology file step by step;
starting with the protein and the heme (and see if it works). I run pdb2gmx,
with CHARMM 27 FF on
Dear gmx users,
I'm working on simulating a protein with two cofactors (hem and
tetrahydrofolat) and its substrate. I'm in the first stage; generating
topology. I choose CHARMM27 as a force field and I'm little bit confused on how
to generate tetrahydrofolate's topology.
I tried the
Dear gmx users,
I'm working on simulating a protein with two cofactors (hem and
tetrahydrofolat) and its substrate. I'm in the first stage; generating
topology. I choose CHARMM27 as a force field and I'm little bit confused on how
to generate tetrahydrofolate's topology.
I tried the online
Dear all,
Thank your for your answers.
@ Justin,
Actually I was hesitating between CHARMM and Amber force fields, I hadn't
enough informations from my tutors. Finally I'm going with CHARMM 27, it is the
most convenient in my case.
Thank you again for your orientation.
Zeineb.
Dear all,
Thank your for your answers.
@ Justin,
Where can I found informations related to the compatibility of one water type
with the force field that I choose for my protein? in other words "where can I
found information about the water type that had been used for the
parametrisation
Hi,
I'm working on a protein and two cofactors and one substrate, I have too
simulate all this system on GROMACS. I'm in the first stage: choosing a force
field, box type and dimensions, water molecules...etc.
I would like to know more about the water molecule types (I looked on the
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