I’m reading from the restart files and then use ‘fix rigid’. I’m not sure if this is a valid script, because the atoms in the rigid body should not initially straddle the periodic boundary if ‘fix rigid’ is used. How are the coordinates of those atoms in the rigid body stored in restart file? Are they stored in a way that the rigid body is kept as whole or not?
restart files contain atom image flags and molecule IDs. fix rigid will use these pieces of information and the option you choose (i.e. single, molecule, or group) to "glue" atoms into rigid bodi(es) before the simulation starts.
Quoting hong bingbing <[email protected]>:
Trung is correct. There is no conceptual problem
with using fix rigid to define a rigid body that straddles
a periiodic boundary, so long as the image flags for
its atoms are consistent. You can do this from
a data or restart file.
Is there a command having the function of zeroing the total momentum every 1000 steps or 10000 steps or so? Till now I just find ‘velocity zero’ or ‘velocity mom’ can zero the momentum. But each of them can only be used for one step.
Thank you in advance.
Is there a command having the function of zeroing the total momentum every
1000 steps or 10000 steps or so? Till now I just find 'velocity zero' or
'velocity mom' can zero the momentum. But each of them can only be used for