[gmx-users] pdb2gmx: Selecting Force Field in first command

ff to auto-execute remotely. Question Does anyone know how I can pass my Force Field selection from the start? Many thanks in advance! Fernando -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] Atomtype opls_116 not found when runnning GROMPP

Thanks for the fast response, I simply included the forcefield that comes with gromacs after the defaults and commented the defaults from the forcefield, and it ran without a problem. Best Regards Fernando Nunes Justin Lemkul escreveu no dia domingo, 16/06/2019 à(s) 00:38: > > > On

[gmx-users] Atomtype opls_116 not found when runnning GROMPP

009IL/ITP/DCA_scale0.8.itp" #include "oplsaa.ff/spc.itp" [system] ; Name LC, IL, water system [molecules] LC xxx Cation xxx Anion xxx SOL4533 ------ Thanks in advance for your time reading this Best Regards Fernando Nunes -- Gromacs Use

Re: [gmx-users] Extract frames from Trajectory

Try use -dump option and put exact time of the frame you want. Harsha Ravishankar escreveu no dia terça, 27/11/2018 à(s) 15:16: > Hi, > > I need to extract frames from a 100 ns membrane protein simulation > trajectory which contains the protein molecule and lipid molecules which > are at a

[gmx-users] Dihedral Coeffecient Conversion

Hello, I am an undergraduate worker and I am trying to convert a Gromacs Ryckaert-Bellemans form dihedral to AMBER dihedral form. The dihedral I am interested in is: CM-CT-CT-NT 3 3.33465 -1.55226 2.82001 -4.60240 0.0 0.0 ; (From wildcard) amine all-atom This dihedral

[gmx-users] Larger simulation times because of many [ pairs ]?

within or between parts of the system are not required.” Therefore, my question is whether adding a large number of pairs to the list (even when using a single potential table) can result in such a slowdown of the simulations. Thank you, Fernando Yrazu PhD student Rice University -- Gromacs