AMBER Archive (2008)

Subject: AMBER: Heating POL3 Box Troubles

From: Paul Johns (pjohns_at_nd.edu)
Date: Fri Mar 14 2008 - 13:44:44 CDT

I'm fairly new to AMBER, and I've been having some troubles. I have
been trying to run MD on a 40 angstrom box of POL3 water molecules, but
it doesn't seem to be working. In particular, my error comes in when I
try to heat the box of water from 0 K to 300 K. I built the box in Leap
using the leaprc.ff02 force field and the following commands:

WAT = PL3
loadAmberParams frcmod.pol3
solvatebox PL3 POL3BOX 20.0
saveamberparmpol PL3 pol3_2.prmtop pol3_2.inpcrd

This structure seems to be fine, so my next step is minimization. I
minimized rather simply, using the following as the input file:

 &cntrl
  ipol = 1,
  imin = 1,
  maxcyc = 25000,
  ncyc = 10000,
  ntb = 1,
  ntr = 0,
  cut = 8,
 /

A bit excessive on the minimization steps, I know. This seems to be OK,
as well. Now here's my trouble step, heating. I used the following for
the input:

 &cntrl
   ipol = 1,
   imin = 0,
   irest = 0,
   ntx = 1,
   ntb = 1,
   cut = 8,
   ntr = 0,
   ntc = 2,
   ntf = 2,
   tempi = 0.0,
   temp0 = 300.0,
   ntt = 1,
   nstlim = 10000, dt = 0.0002,
   ntpr = 100, ntwx = 100, ntwr = 1000,
 /

When I run this with the output from the previous step, it dies within a
minute of beginning. The end of my output file looks like this:

vlimit exceeded for step 1; vmax = 190.3043
vlimit exceeded for step 2; vmax = 25.7249
vlimit exceeded for step 3; vmax = 22.4714
vlimit exceeded for step 4; vmax = 20.9760
vlimit exceeded for step 5; vmax = 20.4271
vlimit exceeded for step 6; vmax = 20.2735
vlimit exceeded for step 7; vmax = 20.5607
vlimit exceeded for step 8; vmax = 21.2662
vlimit exceeded for step 9; vmax = 22.7314
vlimit exceeded for step 10; vmax = 49.5619
vlimit exceeded for step 11; vmax = 1027.9110
vlimit exceeded for step 12; vmax = **********
vlimit exceeded for step 13; vmax = **********
vlimit exceeded for step 14; vmax = **********
vlimit exceeded for step 15; vmax = **********
vlimit exceeded for step 16; vmax = **********
vlimit exceeded for step 17; vmax = **********

I can't seem to be able to figure out what is going wrong. I tried
doing the same thing for TIP3P just to see if I could get that to work
(not including ipol = 1, and using saveamberparm instead of
saveamberparmpol), and it worked just fine. Does anyone know how to get
this to work with POL3? It shouldn't be that hard....

Paul
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