Re: [gmx-users] Can't observe ion separation under the influence of electric field

in a PBC box. https://www.mpibpc.mpg.de/grubmueller/compel Harutyun Sahakyan Senior Assistant at Laboratory of  Computational Modeling of Biological Processes,  Institute of Molecular Biology, NAS, Armenia, Yerevan Tel: +374 93 323990 h_sahak...@mb.sci.am sahakya...@gmail.com February 13, 2020

[gmx-users] Enforced Rotation

Dear GMX users, I have a question about enforced rotation. I would like to enhance rotation around the peptide bond. Is it possible to rotate only the terminal amino acid (or 2-3 AA) of an unfolded peptide? What kind of rotation should I use in that case? Harutyun Sahakyan Senior Assistant

Re: [gmx-users] ion flux counter

Kutzner, Carsten wrote: > > > > Am 26.09.2019 um 16:24 schrieb Harutyun Sahakyan : > > > > Dear Gromacs users, > > > > Computational electrophysiology protocol has some analyzing tools > allowing > > to count ion flux etc. I have used an external elec

[gmx-users] Fwd: ion flux counter

wishes, Harutyun Sahakyan Senior Assistant at Laboratory of Computational Modeling of Biological Processes, Institute of Molecular Biology, NAS, Armenia, Yerevan Tel: +374 93 323990 h_sahak...@mb.sci.am -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] Young and Cheatham ions parameters for gromacs

Dear GMX users I would like to use Young and Cheatham ions parameters ( https://pubs.acs.org/doi/full/10.1021/jp8001614#si1) with amber99sb-ildn. How can I convert sigma and epsilon values and use them with gromacs? For instance, I want to use K and Cl ions with scpe water, sigma (*R* min/2) and

[gmx-users] »Computational Electrophysiology«

Dear Dr. Kutzner, Thank you for your reply. I have already solved the problem. I made the channels indexing by hand and make a mistake. As a result, split groups were set too close to each other and I got two extremely unequal compartments. I used indexes for channels created with makeSandwich.sh

[gmx-users] Fwd: »Computational Electrophysiology«

any ideas? Have you faced this error before? Channels are defined as several amino acids in the central parts of the channel. I attached my md.mdp file for more detailed information. Thanks in advance. Sincerely, Harutyun Sahakyan Senior assistant at Laboratory of Computational M

[gmx-users] Colchicine topology

Hi all, I use gromacs for MD simulations, but use charmm or amber force fields, did someone try to generate the colchicine topology? I try to do it using CGenFF, but get to high penalty score due to dihedrals. And which force field is better for protein-ligand simulation (tubulin-colchicine)?