Re: [gmx-users] Compile Gromacs with OpenCL for MacBook Pro with AMD Radeon Pro 560 GPU

Hi Szilárd, thank you for the suggestion. I modified the file "src/gromacs/gpu_utils/gpu_utils_ocl.cpp” and replaced both instances of “#ifdef __APPLE__” with “#if 0”. I then checked that the build and regression tests worked without enabling the GPU support. All of the tests passed. Then, in

[gmx-users] Theta and gamma angle between tyrosines

Hi, I have to plot theta and gamma angles between tyrosines throughout the simulation to check if they are involved in pi-pi interactions. I have plotted the centroid distance between tyrosines. But don't know which atoms form theta and gamma angle. How to get centroid atom for tyrosine using

[gmx-users] Hydrogen bond in z direction

Dear all I want to calculate the number of hydrogen bonds in z direction of simulation box, in that, the number of hydrogen bonds versus z direction Would you mind let me know how to do it? thanks -- Best Regards, Mostafa Fakhraee === PhD Student of

[gmx-users] gmx select

Hi all, I am running the gmx select command to obtain all my ligand molecules that are within a cut-off distance from the COM of a protein residue as a function of time. The output from the command below comes with just the atom positions of my ligand. gmx select -f protein_gly.gro -s

Re: [gmx-users] salvation free energy - gmx bar

Hello Shadfar, Check your mdp files for missing/repeated init-lambda-state. I had the same problem, in my case I had two xvg file corresponding to the same init-lambda-state and in consequence one of them was missing Cheers Javier Date: Thu, 11 Jan 2018 23:33:28 + > From: "Shadfar, Shamim"

Re: [gmx-users] Compile Gromacs with OpenCL for MacBook Pro with AMD Radeon Pro 560 GPU

We had some issues with the OS X OpenCL compilers being "special" and not accepting standard ways of passing include arguments. Can you try editing the src/gromacs/gpu_utils/gpu_utils_ocl.cpp file and replace "#ifdef __APPLE__" with "#if 0", compile the code and see if that works? -- Szilárd

Re: [gmx-users] Bond breakage modelling

Thank you Peter, I will try to have a detailed look. Regards, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Peter Kroon Sent: dinsdag 19 februari 2019 13:41 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Bond breakage

Re: [gmx-users] Bond breakage modelling

I've never done it myself, so not really. The manual should help :) I don't know if Morse potentials come built-in, or that you'll need to make tables. Be aware that if you have three or more morse potential particles together they can and will form stable triangles, because there is no

Re: [gmx-users] Bond breakage modelling

Dear Paul, Thank you for your response. Unfortunately, ReaxFF shows some discrepancies in some cases when it comes to carbohydrates. Besides, its parameters are not written for GROMACS. I am looking for maybe a code to mimic this behavior using the validated force fields for carbohydrates, say

Re: [gmx-users] Bond breakage modelling

Hello, in general I would advise not to use a classical force field to model a quantum mechanical effect like breaking a bond. Classical force fields are not parametrized to reproduce those effects, and while you might get something that looks fine with the morse potential it would definitely

Re: [gmx-users] Bond breakage modelling

Dear Peter, Thank you for your prompt reply. I think I can try the morse potential to see how the system responds. Could you kindly provide some more info about how to implement it? Best regards, Ali > On 19 Feb 2019, at 11:35, Peter Kroon wrote: > > Hi Ali, > > > The short answer is "not

Re: [gmx-users] Is there a more efficient way to calculate the "gmx distance" with a very long index?

Can I also ask, I am running it on high performance computer (HPC). So whether the cpu (-pe mpi 12) or memory (-l mem=2G) would influence the capability to handle a very long index file? When the job is submitted, longer queue time will be required if requesting more resources. So I want to

[gmx-users] Minimum distance of ligand molecules

Hi all, For example if I have 200 ligand molecules in my system, is there a way of plotting the identity of those ligands in the form of an index (e.g. 1,2,3, etc...) with minimum distance from the binding sites as function of time? Akash -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Bond breakage modelling

Hi Ali, The short answer is "not really". You could model your bonds as non-bonded (morse) potentials, but then you lose all angle dependence on the potential energy, since the non-bonded potentials must be pair-wise. Depending on the exact problem this may be acceptable though. The angle

[gmx-users] Bond breakage modelling

Dear All, We have simulated a cellulose fiber using GLYCAM06 ff parameters converted to GROMACS. The model is validated and works properly. We are investigating the behavior of the material under tensile load. However, as covalent bonds are modelled with a harmonic potential -as it is in

[gmx-users] analysis following the equlibration of protein-membrane system

Dear Gromacs users, I've performed a membrane-protein simulation by charmm36ff as described below: 1. 10ns of NVT equilibration with position restrained on the protein 2. 50ns of NPT equilibration with position restrained on the protein 3. 200ns of NPT equilibration without position restrained