them from the TPR files or I should
contact the original authors instead?
Thanks in advance,
Jernej Zidar
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Dear Yi,
The easiest way do this would by simply extending the first simulation for
a given number of steps:
- - - script - - -
# run the first simulation
gmx mdrun -v -deffnm md
# continuous running
for i in `seq 2 6`; do
let j=i-1
gmx mdrun -s md.tpr -deffnm md$i -nsteps 2 -cpi &>
Hi,
I have an interesting problem with the NVML library from CUDA 9 (and 9.1)
and Gromacs 2018. Namely, the NVML is reported as detected during cmake but
Gromacs 2018 is linked without it.
This is the cmake command I would issue:
m -rf * && CMAKE_PREFIX_PATH=/home/zidar/utils/fftw-3.3.6-gcc/ \
Dear Jason,
Did you try using a newer version of the GNU compilers (something from the
6.x line for example). New hardware and old compilers may result in poor
performance.
Cheers,
Jernej
>
> --
>
> Message: 1
> Date: Fri, 12
Hi,
I’ve been testing the first beta of the upcoming Gromacs 2018, where one of
the main features is the ability to run compute PME on GPUs. I tried it and
it runs well.
My question is: Would it make sense to get a bitcoin mining rig (4,5 Nvidia
cards, slow CPU) to run simulations in place of
Hi,
I am using 'gmx insert-molecules' to insert ten rather large polymer
molecules into a 16x16x16 nm box. The problem is that the utility inserts
the molecules randomly (which is good) in way that leaves the polymer
molecules sticking outside the defined box and leaving lots of space empty.
The
be missing?
Thanks in advance,
Jernej Zidar
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Hi,
I am trying to solvate a small DNA molecule. Since I don't want so
simulate more waters than what is really neccessary, I decided to try the
dodecahdron and octahedron unit cells.
After I added waters I went to examine the resulting structures in VMD
only to find that the octahedron and
Dear Mark,
Thanks for the explanation.
Best,
Jernej
On Thu, Aug 18, 2016 at 8:22 PM Sorry, there's a typo in how we named that file. I've fixed it for 5.1.4,
> but you need to use
>
> -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-bgclang-cxx
>
> for now.
>
> < snip >
>
> XL compilers on
Hi guys,
I am trying to compile Gromacs 2016 for a Bluegene/Q machine and I've
encountered a small error during the cmake/configure stage:
[ihpczidj@cumulus gromacs-build]$ rm -rf * && cmake ../gromacs-2016
-DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-bgclang-CXX -DGMX_MPI=ON
ven possible without resorting to OpenMPI?
Thanks,
Jernej Zidar
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Hi,
I would like to import several hundred molecules to Gromacs.
I know that one can set the force field "automatically" and pick the
desired water model like so:
echo 16 | pdb2gmx -f some.pdb -water spc
Is there a way to automate the selection of the termini? The proteins I
am importing
Dear Justin,
Thank you.
For posterity, this is how I solved my problem:
echo -e "16\n3\n3\n3\n3" | pdb2gmx -v -f blah.pdb -water spc -ter
Inserting the new lines (\n) helped.
Jernej
5. Re: Automating pdb2gmx (Justin Lemkul)
>
>
> You can echo as many selections as you need.
Hi Mark,
I will send you the files.
I managed to solve the issue by replacing the content of the
~/gromacs-5.1/src/gromacs/simd directory with files from Gromacs
5.0.6. Still curious about what could have caused such an issue.
Best,
Jernej
Hi,
That all seems wildly unlikely,
Hi,
I am unable to compile Gromacs 5.1 using the XL compiler (version 12.1.0)
on our BlueGene/Q cluster.
Before starting I set the relevant paths like so:
export PATH=/bgsys/drivers/ppcfloor/comm/xl/bin/:$PATH
export
LD_LIBRARY_PATH=/bgsys/drivers/ppcfloor/comm/xl/lib/:$LD_LIBRARY_PATH
export
Hi everyone,
Recently I have been reading about clouding computing (specifically
Amazon EC2) and was wondering what is your experience with such services.
My questions are:
1. What is the performance?
2. What is the price/performance ratio?
3. Amazon EC2 allows for GPU computing. Any
Hi Justin,
Thank you for the explanation.
Best,
Jernej
On Fri, Mar 6, 2015 at 11:01 PM,
gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote:
Hi there,
I have a receptor with a docked ligand. I would like to perform an
umbrella sampling simulation to get some insights into the
#pull
I use Gromacs 5.0.4.
Thanks again,
Jernej
On Fri, Mar 6, 2015 at 3:04 PM, Jernej Zidar jernej.zi...@gmail.com wrote:
Hi there,
I have a receptor with a docked ligand. I would like to perform an
umbrella sampling simulation to get some insights into the
thermodynamics of the binding
Hi there,
I have a receptor with a docked ligand. I would like to perform an
umbrella sampling simulation to get some insights into the
thermodynamics of the binding.
Following the Umbrella Sampling tutorial I performed the 500 ps
pulling simulation. A visual examination of the trajectory
Hi everyone!
I would like to study a DNA-protein complex. The protein part is
composed of aminoacids covalently attached to the DNA bases. Which
force field would you recommend? Based on recent experience I was
thinking of using either OPLS-aa or CHARMM. OPLS-aa would be the
prefered choice
Dear Rebeca,
For small organic molecules you should use the portal
www.paramchem.org to do the initial atom typing. Then you can use the
python script found on the website of dr MacKerell
(http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs) to convert
the resulting str file to a
Hi,
Did you try playing around with the number of MPI, thread tasks. I
was actually able to significantly improve the performance.
Try for example overloading both GPUs like so:
gmx mdrun -v deffnm foo -ntmpi 4 -ntomp 2 -gpu_id 0011
or
gmx mdrun -v deffnm foo -ntmpi 2 -ntomp 4 -gpu_id 01
in advance,
Jernej Zidar
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Please please read the basics (i.e. how to use) about Gromacs before
posting questions.
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Hi!
Following Joao's suggestion I went to check all the commands I used,
I realized it was a typo. Namely, I was tellgin g_gyrate to use the
wrong index file with the right trajectory.
Thanks to everyone for helping out.
Jernej
On Fri, Feb 7, 2014 at 4:54 AM,
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