Dear Friends,
I want the suggestion from you on my plan of work. The plan is as
follow :
I have the protein pdb file in which two protein interact with
each other and the dimer
formed. The dimer is responsible for various bad effect in cell. So my aim
is to to inhibit the dimer form
On 01.10.2014 03:52, AINUN NIZAR M wrote:
I'm a newbie in MD. I would like to simulate a protein folding, from a
primary protein structure to a fully-folded state for a wild type and
mutated protein. Then I will compare them and make movie from unfolded to
folded state. I want to use REMD method
That is surprising. I thought intel compiler is the best compiler for intel
cpu.
On Tue, Sep 30, 2014 at 5:40 PM, Szilárd Páll
wrote:
> Unfortunately this is an ill-balanced hardware setup (for GROMACS), so
> what you see is not unexpected.
>
> There are a couple of things you can try, but don't
Hi,
Not really surprising. The compiler teams try to optimize the performance
of lots of different kinds of code on a range of platforms. Some kinds of
code aren't prioritized for a given compiler team. Often there are
trade-offs that mean some kinds of code gets faster while others get
slower, pe
Hi Gromacs users,
The official release of Gromacs 5.0.2 is available! It contains a fix for
a major simulation correctness problem with PME + GPUs in 5.0 and 5.0.1.
Please see the link to the release notes below for more details. There are
also some other minor bug fixes and performance enhancem
I am planning to buy 2x GTX 970 for 5820K overclocked to 4.5 GHz. I have budget
limitations and not able to afford workstations with 2x CPUs. Let me know if
you are aware of any cheaper alternative.
Also let me know if in future Gromacs could become more GPU intensive allowing
more GPUs with
On Wed, Oct 1, 2014 at 5:40 PM, Pappu Kumar wrote:
> I am planning to buy 2x GTX 970 for 5820K overclocked to 4.5 GHz. I have
> budget limitations and not able to afford workstations with 2x CPUs. Let me
> know if you are aware of any cheaper alternative.
Sounds like a good investment!
The only
Hi,
The SIMD-accelerated RB dihedrals got implemented a few days ago and as it
turned out to be a relatively minor addition, we accepted the change
for the 5.0 series and it even made it into today's release!
Expect a considerable performance improvement in GPU accelerated simulations of:
* of sy
Dear Gromacs experts:
I'd like to add the time-dependent function to the electric field routines
in GROMACS.
I could only found the input (reading) codes in src/kernel/readir.c.
Does anyone know which source cord routines I should modify to add the
time-dependent functions.
Thank you for advance.