Re: [gmx-users] Installing/Uninstalling

You can Install without uninstalling in different path, -DCMAKE_INSTALL_PREFIX=xxx -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] radius of gyration in REMD of protein

Hi, I am running a REMD of a protein, which ranged from 270 to 500K in explicit water model with 60 replicas, and I stop to analyse the REMD data after running for 50ns. I use the demux.pl script to get the continue the coordinate for each replica. Then I calculate the Rg value for each

Re: [gmx-users] Problem compiling on Bluegene/Q

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

Re: [gmx-users] Gromacs 2016 building issue

I thought the "build" directory had to be *outside* the gromacs source directory. Don't know for sure if that makes a difference. 2016-08-18 18:20 GMT-05:00 Quentin Kaas : > Hi Mark, > > Thank you for your answer. I just have redone again everything but I get > the same

Re: [gmx-users] Gromacs 2016 building issue

Hi Mark, Thank you for your answer. I just have redone again everything but I get the same problem. I am not even compiling with MPI or GPU support and I have the same. Hereis my procedure: """ tar xzvf gromacs-2016.tar.gz cd gromacs-2016 mkdir build

[gmx-users] Installing/Uninstalling

HelloI have Gromacs 4.5.4 installed (without the MPI enabled for multiple machines) on a Fedora 18 OS; but would like to install Gromacs 5.0.4 with MPI enabled. I want to run REMD simulations and it is my understandingthat I need MPI enabled (even for a quad-core machine) to run separated

[gmx-users] GROMACS performance :installation

Dear all, We have following workstations 2 x 12 core processor + 3 x GTX 980 Ti 2 x 12 core processor + 3 x GTX 1070 2 x 8 core processor + 2 xGTX 1070 and Tesla K20 and a Desktop system with Single i7 processor (8 core) + GTX 1070 Previously I installed with flag DGMX_GPU=ON

Re: [gmx-users] Diffusion coefficient water

The following paper may also be interesting. "System-size corrections for self-diffusion coefficients calculated from molecular dynamics simulations: The case of CO2, n-alkanes, and poly(ethylene glycol) dimethyl ether" J. Chem. Phys. 145, 074109 (2016); http://dx.doi.org/10.1063/1.4960776

Re: [gmx-users] Problem with binding energy

Hi Justin, Yes I am, doing 3 single point simulation but using a very long winded way of doing single - point energy. The DFT calculation gave me -357 kJ/mol, the other software I mentioned is Forcite, which gave me around -250 kJ/mol. Ben From:

Re: [gmx-users] Diffusion coefficient water

See the following paper (http://pubs.acs.org/doi/abs/10.1021/ct400109a) for some examples of diffusion calculations in GROMACS. The finite size correction for diffusion coefficients is something different than the long range energy corrections. A discussion of this (I can't vouch for all the

Re: [gmx-users] Diffusion coefficient water

Hi, I would also consider using a pressure-coupling algorithm that isn't known to create the wrong velocity distribution. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Diffusion coefficient water

On 8/18/16 6:48 AM, Diez Fernandez, Amanda wrote: Thanks Justin and Nikhil, 1) So in principle is it expected that results will be different and I should take my final value to be the average of, say, 10 simulations? Yes, averaging over multiple, independent simulations is the correct

Re: [gmx-users] Problem with binding energy

Apologies those were negative values. On 18 August 2016 at 22:21, Billy Williams-Noonan < billy.williams-noo...@monash.edu> wrote: > So gromacs gives an answer of 6000 kJ/mol and some other software using > the same method yields 250 kJ/mol ? > > On 18 August 2016 at 22:13, Ben Tam

Re: [gmx-users] Problem with binding energy

On 8/18/16 8:13 AM, Ben Tam wrote: Hi Billy, To be more exact, the system has been energy minimised through DFT calculation. We want to compare that with MM force field by using the same co-ordinate. Henceforth we don't need an average gibbs energy but one specific frame energy

Re: [gmx-users] Problem compiling on Bluegene/Q

Hi, On Thu, Aug 11, 2016 at 9:05 AM Jernej Zidar wrote: > 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

Re: [gmx-users] Problem with binding energy

So gromacs gives an answer of 6000 kJ/mol and some other software using the same method yields 250 kJ/mol ? On 18 August 2016 at 22:13, Ben Tam wrote: > Hi Billy, > > > To be more exact, the system has been energy minimised through DFT > calculation. We want to compare

Re: [gmx-users] Gromacs 2016 building issue

Hi, GROMACS 2016 doesn't use libxml2 at all, so it looks like there's something strange going on with how you've done that build, because there's no way the template can have such a linking dependency. Mark On Thu, Aug 18, 2016 at 2:43 AM Quentin Kaas wrote: > Hello, > >

Re: [gmx-users] CPU running doesn't match command line

Hi, It's a bit curious to want to run two 8-thread jobs on a machine with 10 physical cores because you'll get lots of performance imbalance because some threads must share the same physical core, but I guess it's a free world. As I suggested the other day,

Re: [gmx-users] Problem with binding energy

Hi Billy, To be more exact, the system has been energy minimised through DFT calculation. We want to compare that with MM force field by using the same co-ordinate. Henceforth we don't need an average gibbs energy but one specific frame energy calculation. Best regards, Ben

Re: [gmx-users] Problem with binding energy

Hi Ben, My understanding of what you've done is that you have calculated a binding enthalpy for the water at a specific, non-biological temperature, and not a Gibbs free energy that you would expect from experiment... Billy On 18 August 2016 at 21:34, Ben Tam wrote:

[gmx-users] Problem with binding energy

Dear all, I have a problem with calculation with binding energy with using gromacs. My calculation is the binding of solvent onto a crystal. The steps I took to calculate binding energy is like this: 1) Energy minimised my crystal system with the solvent. 2) Calculated the energy of the

Re: [gmx-users] Fwd: is there martini CG parameters for K+ ion?

Hi, disturbing to hear you can't register on our forums. We've been having some trouble with the website, so we'll definitely look into it. As for the science: Na+ and K+ are identical in Martini. The size difference is compensated by the implicit solvation shell anyway. You'd have to look into

Re: [gmx-users] Diffusion coefficient water

Thanks Justin and Nikhil, 1) So in principle is it expected that results will be different and I should take my final value to be the average of, say, 10 simulations? 2)If so, the average over my simulations is not similar to the published average. They also use a unit cell of 216 molecules (I

[gmx-users] MM/PBSA for protein-membrane system

What is the possibility of using MM/PBSA method for calculating interaction energy between Protein and membrane? -- Regards, Nikhil Maroli -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?