Re: [gmx-users] gromacs 2018 with OpenMPI + OpenMP

> Are you sure that's better than mdrun's internal thread binding? yes even with warnings I see better performance, so surely if we can remove warnings and bind properly we will see much better performance than thread MPI. On Thu, Dec 13, 2018 at 3:41 AM Szilárd Páll wrote: > On Wed, Dec 12,

[gmx-users] duplicated position restraint statements

Hi all, Quick question: in some of our models, the list of position restraints as part of the permanent topology is created externally, based on the atomic positions. Unfortunately, there is a slight bug in the restraint generator and for a small portion of the restrained atoms the statements

[gmx-users] Phosphorylation Atom Parameters in Implicit Water

Dear All I am facing problems about phosphorylation of amino acid. I use implicit water model for MD in gromacs 4.6.7, but I lack parameters about phosphorylation in gbsa.itp (i.e. OS and P atomtype parameters). Is there any references I can get? Yours sincerely, Tang -- Gromacs Users

[gmx-users] Why charge parameter of cations like Cu2+, Zn2+ in GROMOS 54a7 force field in GROMACS equals to zero?

Hi all, I am trying to modify the original GROMOS 54a7 force field files implemented in GROMACS to add parameters of some new cations. But when I checked the ffnonbonded.itp, I found that the charge parameter of CU2+, Zn2+ equals to zero. Why? What does it mean? How GROMOS 54a7 force field

[gmx-users] Epsilon_r

Dear Gromacs Users, How do we determine the epsilon_r for a MD simulation? If we do a MD simulation for a system with some molecules in water, what is the value for epsilon_r? Is it equal to the relative dielectric permittivity of water? Thank you. -- Gromacs Users mailing list * Please search

[gmx-users] is acpype compatible with amber 2018?? parmchk2 and not parmchk available

Dear Experts, Has anyone with amber 2018 able to generate ligand topologies for Gromacs simulation. I got an error reporting "parmchk failed" while executing "acpype -i FFF.pdb". I noticed that there is no "parmchk" installed in the system. The current version installed during installation of