I had a similar issue with dssp which suddenly stopped working. Switching
to x86 binary worked for me.
Linux Arch
Mat
On Tue, 13 Mar 2018, 09:25 Joe Jordan, wrote:
> You can find a dssp binary here http://swift.cmbi.ru.nl/gv/dssp/
> It is also in the ubuntu repo.
> You should to get mkdssp and
I am simulating metallic surface together with proteins and I need to use
atom freezing to ensure that the pressure calculation is correct.
In the documentation the user is told to use "energy group exclusions"
together with freezing atoms. However, the "energygrp-excl" does not work
together with
Dear Gromacsers,
After compiling gromacs successfully with SSE4.1 it suggested AVX_256
instead. With AVX_256 the compilation is interrupted with the FFTW error
below. In this case I am in need of more CPU power due to the multiple GPUs
installed.
--
moved the issue.
Thanks, Mat
On Thu, Jun 21, 2018 at 11:04 AM Mateusz Bieniek
wrote:
> Dear Gromacsers,
>
> After compiling gromacs successfully with SSE4.1 it suggested AVX_256
> instead. With AVX_256 the compilation is interrupted with the FFTW error
> below. In this case I am in nee
Hi Chetan,
You might consider also using MDAnalysis which has a nice little tool just
for this. Here is an example I placed on researchgate:
u=MDAnalysis.Universe("filename.gro")
selected = u.select_atoms("resid 10-15")
selected.write("existing.ndx", mode="a", name="ids10to15")
If you don't have
Extending this question. I understand that the GPU P100 here has internal
CPUs on board. Could Gromacs developer share whether the software is
currently capable of using CPUs inside of a GPU?
Thanks, Mat
On Thu, Jul 12, 2018 at 3:24 PM Szilárd Páll wrote:
> If price does not matter, get V100s;
Hi Andrew,
I cannot answer your question about gmx distance but I have been using the
MDAnalysis package for this kind of analysis. I am writing this in case you
are proficient in python and need more flexibility. The code more or less
would look like this:
u=MDAnalysis.Universe(gro, xtc)
g1 = u.
Hi Rahul,
I've run into a similar issue a year ago. It is possible to configure gmx
with the extra configuration file (as described in the documentation) to
get this right.
However, I found it to be archaic and wrote my own quick DSSP visualiser in
matplotlib.
I am planning to improve the code a
Hi Hadi,
To freeze atoms you have to first create the right group in your index file
.ndx. Then, you use this:
freezegrps = slab
freezedim= Y Y N
Where the Ys refer to X Y Z, meaning here the slab group is frozen in X Y
dimension but not Z dimension.
Please not tha
Sent from my iPhone
>
> > On Mar 20, 2019, at 4:07 PM, Mateusz Bieniek
> wrote:
> >
> > Hi Hadi,
> >
> > To freeze atoms you have to first create the right group in your index
> file
> > .ndx. Then, you use this:
> >
> > freezegrps
> Now I need to freez some atoms that I have their index in a file like
> > freez.ndx. How should I change this mdp file? In other word, which
> option I
> > should add to this file?
> >
> > Thank you once more,
> > Hadi
> >
> > On Thu, Mar 21, 2019 at
Hi Neena,
The position restraint file is a bit of a new concept. It's the
"positions/coordinates" around which the restraints should be applied. That
means your posre.itp file was found and requires now the coordinates around
which to apply the restraints.
Most often people will use their initial
Yes, the 36m (CHARMM36m) is the new set of parameters recommended by the
authors, so it is best to stick to the recommendation unless you know
exactly what you are doing.
Huang, J. et al., 2016. CHARMM36m: an improved force field for folded and
intrinsically disordered proteins. *Nature Methods*,
nteractions the most basic
interactions that you would expect gromacs to calculate?
Regards,
Mateusz Bieniek
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Hi Gromacs,
A small digression: Ideally Gromacs would make it more clear in the error
message explaining which part is not implemented for the GPUs.
Thanks, Mat
On Thu, 12 Dec 2019 at 13:01, RAHUL SURESH wrote:
> Hi John
>
> Thank you and adding here the mdp settings
>
> title = Protein-
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