AMBER Archive (2008)

Subject: AMBER: pmemd iwrap trouble

From: Lars Skjærven (lars.skjarven_at_biomed.uib.no)
Date: Mon Aug 25 2008 - 05:25:09 CDT

Dear Amber users,

I've been running a MD-simulation for about 40ns and needed to wrap
the water back into the primary box (due to water has swimed too far
away). As recommended on the mailinglist I used iwrap for only one
step:

Wrap it
 &cntrl
  imin= 0, irest= 1, ntx = 5,
  ntb = 1,
  cut = 10,
  ntc = 2, ntf = 2, tol = 0.000001,
  ntt = 0,
  nstlim = 1, dt = 0.001,
  ntpr = 1, ntwx = 1, ntwr = 5,
  ioutfm = 1, iwrap = 1,
 &ewald
  dsum_tol = 0.000001,
 /

The restart file produced by this run has about 50% of the solute
outside the waterbox (when visualized in vmd). I can still carry on my
MD-runs (with iwrap=0) after this, but I am worried about the new
coordinates for the solute with respect the the water.

However, when I do reimage in ptraj it seems to be ok:
center :1-224
image familiar
trajout test.rst restart

It must be said I use an octahedral water box. Both pmemd9 and 10
yields the same results for me with this respect.

To wrap it up:
- should iwrap=1 with pmemd10 work when using a octahedral box ?
- or should I use ptraj to reimage? if so, are the velocities ok ?

I realise this is a topic that has been discussed on the mailinglist
earlier and I apologise if my questions are redundant. I searched, but
did not find a clear answer on this..

Best regards,
Lars Skjaerven
University of Bergen, Norway
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