Hi,
I want to do dPCA analysis but I don’t index backbone and khi dihedral in RNA.
Gmx mk_anandx do this but in its out file there are many index that I don’t
find my favorite dihedral. Please gave me some advice.
Thank you.
--
Gromacs Users mailing list
* Please search the archive at
Hi,
This isn't a problem. Thread-mpi is the built-in mpi parallelization
packaged with gromacs. What that message is saying is that Gromacs will use
the openmpi library on your system instead, which is what you want when
running on multiple nodes.
Kevin
On Wed, Aug 15, 2018 at 1:50 PM, Jost,
Hello,
I would like to install GROMACS on a cluster of Volta nodes. I have
openmpi_3.1.1
and
pgi_openmpi_2.1.2
available. For of them I get the message
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
However, I really would like to have this to take advantage of all 8 GPUs
Have
Dear all,
In accessing to a supercomputer facility, I have been asked to estimate how
much computer resource (time and processors) I would need for a MD
simulation project, so, I wonder how I can roughly overestimate what the
project need?
Just to give a hint/example below is the time accounting
On 8/15/18 9:08 AM, Mahdi Sobati Nezhad wrote:
Excuse me I don't understand completely, I residue I see Gua and Ade. You
say I change Gua base with Ade base in the ATPs residue?!
What about my hydrogen bonds?!
Do my charges don't change?!
Additive force fields are constructed from building
Excuse me I don't understand completely, I residue I see Gua and Ade. You
say I change Gua base with Ade base in the ATPs residue?!
What about my hydrogen bonds?!
Do my charges don't change?!
Thanks for your help
On Wed, 15 Aug 2018 16:00 Justin Lemkul, wrote:
>
>
> On 8/15/18 3:05 AM, Mahdi
Hello everyone,
I have a problem using tpic. Basically following the process here:
https://groups.google.com/forum/#!topic/archive-gmx-users/hh2cq9ZtqgU
My system is a surface in contact with liquid water and within which there are
some ions to balance the surface charge. There is a few nm
Hi. I have a triclinic box whose beta angle is 123 making my tilt factor be a
negative value. The rlist,rcoulomb and rvdw depend also on the tilt factor.
This makes it hard to define the coulombic interactions and cut-offs of my
simulation box.
Is there any way on how to get around this?
On 8/15/18 8:11 AM, RAHUL SURESH wrote:
Hi. I tried combining two pdb's such that, 1-24res of PDB X with 25-72 res
of PDB Y. I used pymol to do this. I just aligned the protein in such a way
that the N terminal of one protein is near the C terminal of the other. I
haven't made any physical
Hi. I tried combining two pdb's such that, 1-24res of PDB X with 25-72 res
of PDB Y. I used pymol to do this. I just aligned the protein in such a way
that the N terminal of one protein is near the C terminal of the other. I
haven't made any physical bonds between them and saved as pdb. I have
On 8/15/18 5:47 AM, Yasser Almeida Hernández wrote:
Hi all,
I have two different simulations of a membrane protein in a E. coli
model membrane, and I want to analyze the protein-lipids interactions,
by generating 2D density maps. In each simulation, the protein
moves/rotates different
On 8/15/18 3:05 AM, Mahdi Sobati Nezhad wrote:
hello
I'm working on a protein that contains GTP in its structure. I can't find
any force field that contains GTP's residue but I find a force field that
contains the ATPs residue! There is any way that I can convert ATP to GTP?!
Or any other
On 8/14/18 4:42 AM, Sergio Perez wrote:
Dear grommacs community!
I have some questions about gromacs and I wanted to search within the
mailing list in case the problem had already commed up. But I could not
search easily within a google group like you do in plumed or there was not
a single
Hi,
Paul's answer is fully correct if you are using the (default) appending
upon restart from checkpoint. If you manage the restart or the filenames
yourself, then trjcat -overwrite can be needed because the first trajectory
can have additional frames after the time of the checkpoint (which mdrun
Hello,
I use gmx 2018.1 .I had just done a restart and I then thought that maybe I
could have had that problem and I thought maybe that command could solve
the problem if it had existed. I mean that if in the file there were
overlapping frames they would be overwritten just as if you are doing
Hi all,
I have two different simulations of a membrane protein in a E. coli
model membrane, and I want to analyze the protein-lipids interactions,
by generating 2D density maps. In each simulation, the protein
moves/rotates different along the xy plane of the membrane, and ends up
in a
Hello,
if you restart a run from the checkpoint file than any recent version of
GROMACS will make sure that there are no overlapping frames and that the
continuation is exact.
What were you trying to do on the command line when you wanted to
continue the run, and what version have you been
Dear GMX comunity,
I would like to know if a run is interrupted abruptly (killed by the user)
and then is restarted with -append option, is there any chance that
overlapping frames are generated within the .xtc file?
If this were to happen, would
gmx trjcat -f trj.xtc -o trj2.xtc -overwrite
I have a .gro file in which the atoms and the box size is a rectangular cube,
and I need to change it to a cube. How can I do that?Best
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read
hello
I'm working on a protein that contains GTP in its structure. I can't find
any force field that contains GTP's residue but I find a force field that
contains the ATPs residue! There is any way that I can convert ATP to GTP?!
Or any other idea?!
(I work with gromos 43a1 force field)
thanks
--
20 matches
Mail list logo
