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
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
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
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
Dear Justin,
Thank you for your help!
Cheers,
Mah
On Thu, Jan 1, 2015 at 10:07 PM, mah maz wrote:
> Thanks Justin! I tried the freezegrps and freezedim but it needed the name
> of the groups. As I said in my system only one type of atom is defined.
> Should I put the desired atoms in a differen
On 1/1/15 1:37 PM, mah maz wrote:
Thanks Justin! I tried the freezegrps and freezedim but it needed the name
of the groups. As I said in my system only one type of atom is defined.
Should I put the desired atoms in a different group and freeze them? Any
other ways to call the atoms by their num
Thanks Justin! I tried the freezegrps and freezedim but it needed the name
of the groups. As I said in my system only one type of atom is defined.
Should I put the desired atoms in a different group and freeze them? Any
other ways to call the atoms by their numbers?
Regars,
Mah
On Thu, Jan 1, 2015
On 1/1/15 12:36 PM, mah maz wrote:
Dear all,
I want to have different situations for different atoms in my system. In
the .mdp file how can I freez some of the atoms? ( I dont have residues in
the system; 3 kinds of atoms are present just by one atom type name) Is it
possible to assign differe
Dear all,
I want to have different situations for different atoms in my system. In
the .mdp file how can I freez some of the atoms? ( I dont have residues in
the system; 3 kinds of atoms are present just by one atom type name) Is it
possible to assign different situations to some of the atoms by w
