Re: [gmx-users] NPT equilibration without pbc

Thanks for your input. I am studying how a nano droplet spreads on a substrate. I have created a four atomic layer thick FCC lattice surface on which I have introduced water molecules. The entire system is placed inside a box of dimensions 15 nm X 15 nm X 10 nm. The system is similar to the one

[gmx-users] membrane proteins simulation

Dear all users, I am new in membrane proteins simulation. I want to simulate a membrane protein that it is a part of a large protein and has a big extracellular part.Here is my question: is it ok, I just simulate the membrane part even it is a part of a large protein? and if the answer is

Re: [gmx-users] NPT equilibration without pbc

Once again, please describe your system in more detail, because this isn't about Gromacs (which will correctly refuse pressure coupling for a finite, deep-nanoscale system). It is about the meaning of where pressure comes from in simulations and in reality. In a realistic system "1 bar" would

Re: [gmx-users] NPT equilibration without pbc

Hi Alex, Like I mentioned, my system consists of a water nano drop on a substrate. I need my system to be at 1 bar and 298 K. Without pressure coupling, I am unable to set the pressure to be at 1 bar. On 4 March 2017 at 22:18, Alex wrote: > 1. Could you please provide a

Re: [gmx-users] NPT equilibration without pbc

1. Could you please provide a physical equivalent of a non-periodic NPT system? 2. Why can't you turn off the barostat, like GMX is asking? Alex On 3/4/2017 8:40 PM, Rajorshi Paul wrote: I am trying to simulate water nano droplet spreading on an FCC crystal substrate. I have not implemented

[gmx-users] NPT equilibration without pbc

I am trying to simulate water nano droplet spreading on an FCC crystal substrate. I have not implemented periodic boundary conditions as my system is non-periodic. But when I tried to equilibrate my system in NPT ensemble, the program gives me a warning that I should set pressure coupling as "no".

Re: [gmx-users] linking error while trying to build gromacs

Hello, FYI, problem was solved by building gromacs by another linux user. I have no idea what was wrong with this user. Thanks for trying to help. Andrey 04.03.2017, 01:54, "Mark Abraham" :Hi,That's a cmake log for a different run (building fftw via GROMACS vs not).But I

[gmx-users] RDF calculation

Dear gmx-users, I am new to Gromacs. I have a droplet including some types of lipids such as DPPC. I want to calculate RDF for head atom of DPPC with respect to droplet center-of-mass. My question is how can i calculate this issue in versions 2017. Apparently this feature has been removed from

[gmx-users] UMBRELLA SAMPLING

Hi gromacs users, I want to calculate delta G for protein ligand binding. Had run the umbrella pulling simulation for 100 ps (protein ligand solvated in water), applying restraint in the protein (using the code in gromacs tutorial website, Bevenlab). But, after running the perl script