Hi,
thanks Szilárd for the comment.
About changing the version string, which would be the right place to do it
in the code?
About the last point, do you mean that we should try to put our code into
gromacs main trunk? This would be very nice for us (plumed developers), and
we discussed several t
Dear Mark,
I will go for version 5.1.4 test whether the pairs_nb statement is valid.
Thanks for you help and let me report to you soon.
Adolfo
> Hi,
>
> When you're using a version of the software that's more than three years
> old, and a bug was fixed less than two years ago, you need to get an
Hi Justin
Bouncing back on your early answer about gmx distance, I noticed something
strange (to me)
I'musing the same instruction for a protein file prot.gro
gmx distance ... -select "com of group 'Protein' plus com of group 'Ligand'"
and now I'm running umbrella sampling with pull code st
Dear Mark,
Again, thanks for the reply.
You said I should identify groups of molecules that are to my
interest. I'm unsure how to do this.
My .gro files show no distinction between different molecules, all of
them are built the same (rows deleted for clarification).
1EthBC1 5963 18.910
(previous mail was sent prematurely, my apologies)
Dear Mark,
Again, thanks for the reply.
You said I should identify groups of molecules that are to my
interest. I'm unsure how to do this.
My .gro files show no distinction between different molecules, all of
them are built the same (rows delete
Hi Szilárd,
Many thanks for the idea to keep the multiple versions!
Gregory
On 3/2/17 2:22 PM, Szilárd Páll wrote:
Hi Gregory,
If you have installed in the default system location, you definitely
should clean up before you install a new version (if you did not
change the default path, you ca
On 3/2/17 11:31 PM, Мижээ Батсайхан wrote:
Dear Justin,
Thank you very much.
I analyzed 1001 frames of trajectory. All outputs are written in separate
files. How can I summarize over all time?
They're all just plain text files, so use any scripting language you like to
compile the statisti
On 3/3/17 1:49 AM, Amir Zeb wrote:
Hi Dr. Justin,
I'm wondering that you have mentioned CHARMm27 is not a valid identifier of
protein forcefield, but we have so many articles already published while
using CHARMm27 ff. Can you please let us know how to trace this
unsuitability of CHARMm27 espec
On 3/2/17 11:28 PM, Jonathan Saboury wrote:
I think I narrowed it down to the problem. This time I only simulated MIY
in water and the problem occurs in gmx solvate and gmx grompp
gmx solvate seems to only reads a max of 3 chars for atom type/number (not
sure the correct name, it is the 3rd en
On 3/3/17 5:38 AM, CROUZY Serge 119222 wrote:
Hi Justin
Bouncing back on your early answer about gmx distance, I noticed something
strange (to me)
I'musing the same instruction for a protein file prot.gro
gmx distance ... -select "com of group 'Protein' plus com of group 'Ligand'"
and now
On Fri, Mar 3, 2017 at 11:50 AM Kamps, M. wrote:
> (previous mail was sent prematurely, my apologies)
>
> Dear Mark,
>
> Again, thanks for the reply.
>
> You said I should identify groups of molecules that are to my
> interest. I'm unsure how to do this.
> My .gro files show no distinction betwee
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
Sorry for the delay, but I wanted to add a few points to this discussion
as I am doing my PhD in the group where dPCA was developed.
I hope these will clarify a little bit what's done in the tutorial and
why (took me a while to figure it out).
Obviously, it would be worth to rewrite my comments in
Dear gmx-users,
The radial distribution function with respect to center-of-mass was computable
in old gromacs versions. How can I calculate that in newer version(5.1..)?
Thanks in advance.
Maryam
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Thanks Mark.
I tried gcc 4.9 and used it as follows:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/home/mohsen/programs-mohsen
-DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9
-L/usr/lib/gcc/x86_64-linux-gnu/4.9"
I tried
Hi,
So that means your gcc 4.9 works, but something about the cuda or build
system doesn't work right in such an old (and slow) version of Gromacs.
Ubuntu 16.04 ships a new version of glibc which could also be a problem.
The error is probably not a problem, but we would be interested to see
mdrun
HI, Thanks for yuor reply. Here is log of my cmake output. I can't find anything significantly wrong there. Andrey 03.03.2017, 10:39, "Mark Abraham" :Hi,The simplest explanation would be that your C compiler and your C++compiler are somehow incompatible. But we'd have to see eg the terminal logfrom
On 3/3/17 11:28 AM, zeineb SI CHAIB wrote:
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
- Densit
Hi,
That's a cmake log for a different run (building fftw via GROMACS vs not).
But I can build and install the 5.1.4 tarball fine with the stock gcc 5.4.0
on ubuntu 16.04.02 and cuda 8.0, with or without building ffftw via GROMACS.
Mark
On Fri, Mar 3, 2017 at 9:26 PM Толстов Андрей wrote:
> HI
Hi,
For the record, with GROMACS 4.6.7, the gcc 5.4.0 in ubuntu 16.04.2 with
CUDA 8.0 installed and past tests perfectly for me on a 24-core AMD
dual-GPU node, with and without the own-fftw option. So something about
your machine looks fishy. You should not need to provide linker flags, but
they s
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