Fwd: Periodic cell has become too small

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Dec 24 2009 - 03:49:16 CST

Below " holding the 310K temperature" should be read

"binVelocities $inputname.restart.vel"

which should correspong to a teperature of 310K.

Correspondingly, I commente out:

"# temperature $temperature"

Sorry for previous misinformation


---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Thu, Dec 24, 2009 at 10:35 AM
Subject: Periodic cell has become too small
To: NAMD <namd-l_at_ks.uiuc.edu>


I have minimized a CG system of protein+bilayer+watersolvation with
protein+bilayer fixed

# Minimization
if {1} {
minimize            1000
reinitvels        $temperature

run 25000

bringing it to 310K slowly:

# Gradual increase of temperature
if {1} {
reassignFreq      500
reassignTemp     10
reassignIncr     10
reassignHold    310

Then I tried to equilibrate the system, with same restraints, holding
the 310K temperature, disabling useFlexibleCell ad setting "margin 5".
After new 1000 steps of minimization, the run crashed with:

Periodic cell has become too small.

Any suggestion how to make the equilibration smoother (I guess that
there are too sudden changes) from users that came across a similar
problem would be welcome.

francesco pietra

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:38 CST