AMBER Archive (2009)

Subject: Re: [AMBER] RE: question

From: rrd (rrd_at_seznam.cz)
Date: Wed Nov 04 2009 - 20:52:04 CST

Hi Ross,

thank you very much for helping us.

How wrote Marek, we have problem with freeze atoms. I use ibelly for it and after simulation, atoms aren't on same place as on the beginning of simulation. For example, I use this input file for heating my system.

-----------------------------------------------------------------------------
 &cntrl
  imin=0,
  irest=0,
  ntx=1,
  ntb=1,
  cut=10.0,
  ibelly = 1,
  bellymask=':LGM,WAT',
  ntr = 1,
  restraintmask=':LGM',
  restraint_wt=2.0,
  ntc=2, ntf=2,
  ntt=3,
  gamma_ln=2.0,
  tempi=0.0,
  temp0=300.0,
  nstlim=50000,
  dt=0.001,
  ntpr=5000,
  ntwx=5000,
 /
-----------------------------------------------------------------------------

According to ibelly and bellymask, only residues who can move are LGM and WAT (LGM with restraint), but result is different (see pictures - links below - which show states freeze atoms before simulation and after). On pictures, points are C atoms (without charge) and on top are H-O-H atoms (with qH=0.053, qC=-0.106). For simulation I use sander.MPI.
Do you have any idea why atoms are not freeze? Maybe I do something wrong or I forgot something.
I tried start simulations with much smaller time step and it seems that atoms are really freeze (maybe in longer simulation not) with time step 10 times smaller, so this way it is very painful.

Again, really thank you for any advice.
Pavel

Pictures:
http://physics.ujep.cz/~pcerny/before.png
http://physics.ujep.cz/~pcerny/after.png

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