[gmx-users] Directional Thermostat in GROMACS

Hi, I want to implement a directional thermostat in GROMACS. But I am not sure which files I will need to modify. Can anyone help me with this. I am using GROMACS 4.5.1. Thanks. Apoorv -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please s

[gmx-users] Source Code for Lennard jones truncation schemes

Hello, I was wondering where can I find the source code where the different cut-off schemes (cut-off, shift, switch etc) for lennard jones interactions have been implemented. Thanks. Apoorv -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Ple

Re: [gmx-users] How to control the temperature when using an electric field?

In GROMACS, I believe that whenever an external force is applied, the mean velocity of the group is subtracted before rescaling the velocities and then the mean velocity is added back in. So if you are expecting a plug like flow then there should not be any problem. In other cases also, it should

[gmx-users] Spatially Varying External Force

Hello, Is there a way we can apply a spatially varying external force in GROMACS. I went through the manual if anything like this is possible but couldn't find anything. Any help is appreciated. Apoorv -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

[gmx-users] Forces with Constraints

Hello GROMACS users, I am trying to compute PMF profile for water by integrating the force profile along a given direction. I take the forces directly from MD. I am using SETTLE for constraining the geometry of water molecules (SPC/E model). My question is that do these forces include the constrai

[gmx-users] Source Code for Lennard Jones Interaction

Hello, I was wondering where can I find the source code for the Lennard Jones interaction (both simple cut-off and shifted cut-off) implemented in GROMACS 3.3. Thanks. Apoorv -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

[gmx-users] Thermostating in NEMD

Hi, I was wondering how does a thermostat work in a Non Equilibrium Simulation(NEMD) in GROMACS. Does it subtract out the streaming velocity before applying the thermostat or does it not apply thermostat at all in the direction of the applied acceleration? Thanks. Apoorv Kalyankar Graduate

[gmx-users] Nose-Hoover Thermostat for Non Equilibrium Simulations

Hello GROMACS users, I have a questions regarding how a Nose-Hoover thermostat works in non equilibrium simulations in GROMACS . If I apply some constant acceleration in the x direction, is the thermostat applied to all degrees of freedom or is it applied only in the y and z direction. Thanks. Ap

[gmx-users] Non Equilibrium MD

Hello, I have two questions regarding non equilibrium MD simulations in GROMACS. 1) If we use a thermostat (with T=300 K), will it subtract the non zero streaming velocity to maintain the temperature or will it reset the total velocity. 2) How do we remove the COM motion only due to thermal noise