AMBER Archive (2004)

Subject: AMBER: const-P MD at high T

From: MURAT CETINKAYA (cetinkayam_at_psu.edu)
Date: Mon Oct 18 2004 - 10:27:49 CDT

Dear Amber users,

I am trying to run 1ns simulations on my explicitly solvated protein system. But
when I try to run sander with high system temperatures (more then 500K)sander
gives out an error saying that:

  volume of ucell too big, too many subcells
  list grid memory needs to be reallocated, restart sander
 
I am also aware that the density continuously falls during the constant pressure
run. I have performed constant volume runs (prior to const P run)for at least
100ps (even tried 200ps) but I still get the same result. Here is my input
file:

 &cntrl
  imin = 0, irest = 1, ntx = 7,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 20.0,
  cut = 10, ntr = 0,
  tempi = 600.0, temp0 = 600.0,
  ntt = 1,
  nstlim = 1000000,
  ntpr = 5000, ntwx = 5000, ntwr = 5000
 /

Any kind of help really appreciated...
Thanks,

Murat Cetinkaya
PennState Univ, UP

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