[gmx-users] Suggestion on Simple protocol for MD..

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

Re: [gmx-users] Folding simulation using gromacs

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

Re: [gmx-users] performance 1 gpu

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

Re: [gmx-users] performance 1 gpu

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

[gmx-users] Gromacs 5.0.2 released

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

Re: [gmx-users] Performance of GTX 980 and 970

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

Re: [gmx-users] Performance of GTX 980 and 970

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

[gmx-users] RB dihedral performance greatly improved! [was: Re: GPU waits for CPU, any remedies?]

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

[gmx-users] source cord routines for electric fields

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.