[gmx-users] Energy analysis

Hi gromacs users, I want to calculate the energy for comparative analysis of protein with and without metal ion, wherein I would like to determine the influence of metal on protein structural stability. I have used gromacs for simulation. Please suggest me how to do this kind of analysis? Should

[gmx-users] Turning off electrostatics between protein and water, then protein and protein

Hello, I am running simulations of two protein domains in tip4p water and 0.15M salt concentration that contain up to 650,000 atoms total. The protein domains are separated from each other at the start of each simulation and I am measuring how the distance between them changes over time. Now, I

Re: [gmx-users] Determining the cut offs more than half of the box

Hi, I don't understand what you think you want long cutoffs for. They are baked into the force field and you should not change those without reason to believe it already works. Mark On Sat, 18 Nov 2017 18:08 Iman Ahmadabadi wrote: > Dear Gromacs Users, > > I need

Re: [gmx-users] virtual site, dummy massive site

Hi, Yes those will affect what configurations are sampled, but not the LJ component of the energy of the configurations. Mark On Sat, 18 Nov 2017 23:54 Alex wrote: > And the things that affect the motion of the things with LJ interactions. > :) > > Alex > > > On

Re: [gmx-users] Restarting crashed simulation

Hi, Looks like you made a typo with state.cpt and that you perhaps have multiple mdrun processes running such that the actual output file is in one of the backup files labelled with # characters. Mark On Fri, 17 Nov 2017 19:37 Ali Ahmed wrote: > Hello GROMACS users > My

Re: [gmx-users] virtual site, dummy massive site

And the things that affect the motion of the things with LJ interactions. :) Alex On 11/18/2017 3:49 PM, Mark Abraham wrote: Hi, Only things with LJ interactions can influence the LJ energy. Mark On Fri, 17 Nov 2017 21:06 Faezeh Pousaneh wrote: I have 2 questions

Re: [gmx-users] virtual site, dummy massive site

Hi, Only things with LJ interactions can influence the LJ energy. Mark On Fri, 17 Nov 2017 21:06 Faezeh Pousaneh wrote: > I have 2 questions please. They seem evident, but I need to be sure to > solve my simulation problem: > > 1- Does being a virtual site (charge, no

[gmx-users] Determining the cut offs more than half of the box

Dear Gromacs Users, I need to determine the 2.0 nm for VDW and Coulombic cut offs for my box that its height along z direction is too small (for example 2.0 nm) but the error will arise for me and I couldn't use the cut off more than 1.0 nm because of the box size. What should I do in this

[gmx-users] c_6 and c_12 to zero

Hi, I have a simple system of non-charged diatomic molecule, (A-B). I expect total LJ interaction energy in such system when we put LJ parameters of atom B zero (c6 and c12=0) should be equal with total LJ energy of a system containing only atom A. Am I right? Best regards -- Gromacs Users

[gmx-users] virtual site, dummy massive site LJ interactions

Hi, I have 2 questions please. They seem evident, but I need to be sure to solve my simulation problem: 1- Does being a virtual site (charge, no mass) or a normal atom, effects on its LJ interaction energies with rest of system? 2- Does adding a dummy massive site (no charge, only mass) to