Re: [gmx-users] GROMOS force field for small molecules

On 7/11/19 10:19 AM, Edjan Silva wrote: Dear users, Is the use of the GROMOS force field for small molecules reliable? I performed complex DNA-LIG simulations and noticed slight distortions in the binding angles of some functional groups such as the −C ≡N

Re: [gmx-users] convergence of bilayer simulation

On 7/11/19 12:14 PM, Prasanth G, Research Scholar wrote: Dear Roshan, Thank you for your response. I thought that the lipid also behaves as a solvent in the case of membrane simulation. we even try to make sure the set temperature (starting from equilibration) is beyond the phase transition

Re: [gmx-users] convergence of bilayer simulation

Dear Roshan, Thank you for your response. I thought that the lipid also behaves as a solvent in the case of membrane simulation. we even try to make sure the set temperature (starting from equilibration) is beyond the phase transition temperature. I wonder what sort of impact this will have on

[gmx-users] GROMOS force field for small molecules

Dear users, Is the use of the GROMOS force field for small molecules reliable? I performed complex DNA-LIG simulations and noticed slight distortions in the binding angles of some functional groups such as the −C ≡N

Re: [gmx-users] part of ligand molecule leaves protein

Dear Andrew: You can look at temporal profile of area buried at the protein-ligand interface / protein-ligand coordination number. If there is a sharp change at the beginning of simulation it might be indicative of improper equilibration of complex. A gradual change over initial few nanoseconds

Re: [gmx-users] questions about Ryckaert-Bellemans type dihedrals

Hi, The only thing that matters is that you understand how the force field constructs the interactions, and that your topologies do that :-) Mark On Tue., 9 Jul. 2019, 22:09 Yunhui Ge, wrote: > Hi, > > I have a question regarding Ryckaert-Bellemans dihedral potentials > (function type 3). In

Re: [gmx-users] GPU support on macOS 10.14

Hi, 13-inch MacBook Pros run with an Intel Iris GPU and I wanted to point out that I did not test it with this GPU. Sorry for the missunderstanding. Falk    Gesendet: Mittwoch, 03. Juli 2019 um 17:05 Uhr Von: "Michael Williams" An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] GPU support on

Re: [gmx-users] GPU support on macOS 10.14

Hi Mark and Mike, thank you very much for the answer. I finally managed to compile and use Gromacs (2019.3) with openCL support on my MacBook Pro (2016). However, I still had some errors with the PME calculations after using mdrun. This seems to be a known issue and PME calculations on GPUs

Re: [gmx-users] GPU support on macOS 10.14

Hi Mark and Mike,   thank you very much for the answer. I finally managed to compile and use Gromacs (2019.3) with openCL support on my MacBook Pro (2016). However, I still had some errors with the PME calculations after using mdrun. This seems to be a known issue and PME calculations on GPUs

[gmx-users] part of ligand molecule leaves protein

Hi gromacs users, I did md simulation of the protein-ligand complex. As shown in figure, after 50 ns, part of ligand molecule leaves protein. I remind that I resolve pbc problem at first. https://1drv.ms/u/s!AveJH4Y30cH0tFp_XYCqkrCd7Kqq What is the reason of this state? Best, Andrew --