Re: [gmx-users] atom freezing during simulation

On 5/4/15 1:10 AM, mah maz wrote: Hi Justin, Unfortunately, I am looking at the right atoms! Coordinates of the frozen atoms are different from their initial ones and they have non-zero velocities. I set up the .mdp file as follows: freezegrps = frz1 frz2 freezdim = x y z x y z Is it the corre

Re: [gmx-users] atom freezing during simulation

Hi Justin, Unfortunately, I am looking at the right atoms! Coordinates of the frozen atoms are different from their initial ones and they have non-zero velocities. I set up the .mdp file as follows: freezegrps = frz1 frz2 freezdim = x y z x y z Is it the correct way of setting up frozen groups? Th

Re: [gmx-users] atom freezing during simulation

On 5/3/15 1:17 AM, mah maz wrote: Dear all, I need to freeze some atoms in my system not to move during simulation. I used freezegrps and freezdim options but after simulation, I can see that the fixed atoms also moved and their coordinates changed. What can I do to fix their positions? Should

[gmx-users] atom freezing during simulation

Dear all, I need to freeze some atoms in my system not to move during simulation. I used freezegrps and freezdim options but after simulation, I can see that the fixed atoms also moved and their coordinates changed. What can I do to fix their positions? Should I couple them with thermostat and ass