[gmx-users] fep protocol for gromacs 2016

Hi everyone, I’ve been trying to get a the free energy difference between a leucine residue vs an alanine residue by doing a set of FEP simulations in which I decouple the VDW and electrostatic interactions in the martini CG force field. In the particular example I’m using here, I’m aiming to

[gmx-users] adding windows to thermodynamic integration

Hi everyone, I'm doing a TI calculation for a molecule that's of interest to me and the results after gmx bar processed the dhdl.xvg files aren't so good at certain points so I want to add some lambda values around the problematic ones and I was wondering if this means I have to do the entire

[gmx-users] constraining secondary structure gmx 5

I've been trying to run a gromacs simulation of alternating d/l cyclical peptides (yes I know this is a dead horse that's been beat one time to many...) and after a lot of experimentation I managed to get an initial setup working via charmm gui. However, as the simulation progresses the

Re: [gmx-users] constraining secondary structure gmx 5

al Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Yoav Atsmon-Raz <yoav.atsmon...@ucalgary.ca> Sent: Thursday, December 10, 2

[gmx-users] pdb2gmx (ver 5.0.7) - choosing -ter "None" does not work

Hi, I've been trying to make an peptide with removed amine and Carboxyl terminal groups by applying the -ter "none" option of pdb2gmx. However, everytime I apply it, it fails in constructing the gro file. If I don't use the -ter option it suceeds making the gro file but makes those groups

[gmx-users] using charmm36 force field with gromacs

Hi there, I'm a noob with Gromacs 4.6.7 which is interested in doing all-atom simulations with the charmm36 force field for a protein-membrane system while applying the Verlet cutoff scheme. Basically I have two questions regarding this matter: 1) Does using the CHARMM36 ff necessitates any

[gmx-users] using charmm36 force field with gromacs

Hi there, I'm a noob with Gromacs 4.6.7 which is interested in doing all-atom simulations with the charmm36 force field for a protein-membrane system while applying the Verlet cutoff scheme. Basically I have two questions regarding this matter: 1) Does using the CHARMM36 ff necessitates any

Re: [gmx-users] using charmm36 force field with gromacs

, Yoav Atsmon-Raz wrote: > Hi there, > > I'm a noob with Gromacs 4.6.7 which is interested in doing all-atom > simulations with the charmm36 force field for a protein-membrane system while > applying the Verlet cutoff scheme. Basically I have two questions regarding > this matte