[gmx-users] large pressure
Shuangxing Dai
shuangxingdai at gmail.com
Thu Jul 9 22:46:14 CEST 2009
Hi, all,
I was wondering why I got large pressure after energy minimization. In MD, the pressure and pressure tensor is defined like ( equation 4.151 in manual):
P=2*(E_kinetic + W)/(3*V), V is volume and W is Virial.
I run a simple system, fcc gold with LJ potential to check the pressure after energy minimization. I got:
Pressure (bar)
8.75158e+03
Steepest Descents converged to Fmax < 1 in 1 steps
Potential Energy = -1.4870625e+03
Maximum force = 2.2925207e-05 on atom 1606
Norm of force = 7.9803776e-06
The force is very small and the energy minimization finished in 1 steps, since all the atoms are at equilibrium. So I was wondering why I got this huge pressure. And in a lot of simulations, I found huge pressure after energy minimization. Even in free energy tutorial on Wiki, I found large pressure as larege as 1 GPa. After energy minimization, the forces are very small and no velocity, so the pressure should be close to zero.
Anyone has any idea about this?
PS: Why the forces in traj.trr are all zeros?
This is the mdp file:
; RUN CONTROL PARAMETERS =
integrator = steep
nsteps = 500
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 1
nstvout = 1
nstfout = 1
; Output frequency for energies to log file and energy file =
nstlog = 1
nstenergy = 1
; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol = 1
emstep = 0.01
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 1
; ns algorithm (simple or grid) =
ns_type = simple
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 0.9
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = PME
rcoulomb = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r = 1
; Method for doing Van der Waals =
vdw-type = Cut-off
; cut-off lengths =
rvdw = 0.9
Thanks in advance,
Shuangxing Dai
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