[gmx-users] Implicit solvent improvement in Gromacs 5.1.2

Dear all, There is any improvement of GB implicit solvent in Gromacs package 5.1.2? Regards, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] grompp protein-ligand complex simulation

maybe try to add "" in your .top file. ; Include generic topology for ions #include "oplsaa.ff/ions.itp" On 3 March 2016 at 13:00, Adamu, Aliyu wrote: > Thanks Justin for the response. no my protein does not have any Zn2+ > bound. as for the alteration of files I only added my ligand topology

Re: [gmx-users] Sulfate ion parameters

You may try to generate topology file using Topolbuilder http://www.gromacs.org/Downloads/User_contributions/Other_software Regards, On 24 February 2016 at 14:16, #SUKRITI GUPTA# wrote: > Dear gromacs users, > > > I wanted to simulate sulphate ions in water using oplsaa force field but I > coul

Re: [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble

ain a fine description of what > (conformationally) happen outside your explicitly defined collective > variables. > > Cheers, > Luigi > > > On 13/01/16 14:09, Christian Bope Domilongo wrote: > > Thank you Luiji, > > > > > > > > On 13 January 2016 at 2

Re: [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble

stem at those specific CVs), > 2. select the frames based on the COLVAR files created by plumed and > eventually > 3 extract those frames from the TRR trajectory files. > > If you work in python I would suggest you to take a look at MDtraj > library for extracting the frames.

[gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble

Dear All, I have run my Metadynamics simulation perfectly using plumed. I have check in the tutorial and website to find if it is possible to reweigh my meta trajectory as a function of FES and obtain a average trajectory which is a canonical ensemble. Because the trajectory obtained from plumed

[gmx-users] NPT compress Box using negative Pressure

Dear all, Need help on how to set negative pressure in order to compress the Box. I have used negative pressure (-0.2) but the box is still expending. ; Pressure coupling Pcoupl = parrinello-rahman Pcoupltype = semiisotropic nstpcouple = -1 ; Time con

[gmx-users] GTP and GTP topology for OPLS-AA force field

Dear All, I want to generate topology file for Guanosine-5'-triphosphate (GTP) and Guanosine diphosphate (GDP) for OPLS-AA force field in order to run mmy simulation Groamcs. Any suggestion. Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Suppor

Re: [gmx-users] How to compute persistence length in gromacs

Thank you justin for reply. I have read and follow the second paragraph and use this command *g_polystat -s tmp.tpr -f tmp.xtc -n index.ndx -p persist.xvg* On 30 January 2015 at 19:14, Justin Lemkul wrote: > > > On 1/30/15 3:10 AM, Christian Bope Domilongo wrote: > >> Hi

[gmx-users] How to compute persistence length in gromacs

Hi all, I used g_polystat command in gromacs to compute persistence length and I define atom group in index.ndx file. The result is like Average end to end distance: 0.203 (nm) Average radius of gyration: 0.051 (nm) Average persistence length: *2.00 bonds* (? why not in nm?) Regards, -- Gr