[gmx-users] reciprocal vector of Ewald summation

Dear gmx users, I'm curious about how to determine the magnitude of reciprocal vectors in normal Ewald summation. Take the example in the manual(4.6.5), the box length is 3nm and Fourier spacing is 0.6, then it says there will be 11 wave vectors in each direction. How to get this value? -- Sincer

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian) (andrian)

Hi, Not sure if it was also you, but I recall replying not so long ago to a QM/MM question that all QM atoms must by inside the same topology (itp or top) for gromacs 4 and beyond. Splitting the QM atoms over multiple topologies leads to erroneous behaviour. I don't know for sure if this is a

Re: [gmx-users] g_hbond: range checking error

Hi.. Thanks for the reply. I was unable to download gromacs-5.1.2; when i clicked on the link, it showed "the site can't be reached." However I have been able to figure out the solution. The trajectory file I was using for analysis of protein-solvent hydrogen bonds did not contain water coor

[gmx-users] Fwd: Simulation getting slower and ultimately crashing

-- Forwarded message -- From: soumadwip ghosh Date: Wed, Apr 27, 2016 at 2:52 PM Subject: Simulation getting slower and ultimately crashing To: "gromacs.org_gmx-users" Hi, I am simulating a nucleic acid in the presence of a 15X15 single walled carbon nanotube using CHARMM 2

[gmx-users] gmx densmap tool for the ensemble of the MD trajectories

Dear Gromacs users! To detect different binding sites of the assosiation between two proteins during 10 independent md runs I would like to i) combine all of my MD trajectories together and center the receptor protein {which is consisted of 10 chains determined as 10 .rtp files within topology.t

[gmx-users] simulation_uery

Sir, I am running a simulation for 50ns for a protein separately and also with a ligand docked to the protein. The mdp files and all are same for both the run , but however while running the protein its taking only around 3 days while running the protein-ligand docked complex its taking around 7 da

[gmx-users] .mdp settings for CHARMM36

Hello everyone, I would like to know if the prescribed settings for CHARMM36 (http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM), specifically regarding constraints = h-bonds, apply to all steps (em, nvt, npt, etc). I am assuming so, but I am asking because setting constra

Re: [gmx-users] .mdp settings for CHARMM36

On 4/28/16 5:21 PM, Gregory Poon wrote: Hello everyone, I would like to know if the prescribed settings for CHARMM36 (http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM), specifically regarding constraints = h-bonds, apply to all steps (em, nvt, npt, etc). I am assuming so,

[gmx-users] Unfolding event after restart

Hello, In umbrella sampling simulations I have observed unusual unfolding events, which appear after restarting simulations. I have simulated a homo-dimer with about 150 residues for each monomer. The system has been set up with TIP3P explicit solvent and the CHARMM22* force field. In the umbrell

[gmx-users] questions on ligand.gro and ligand.itp preparation

Dear All, Here I have 2 questions related to the ligand.gro and ligand.itp preparation for the md of protein-ligand complex. First, we have different ways to get the ligand.itp by different serves which use different electronic charge assignment methods. Is any difference for the md result f