AMBER Archive (2005)

Subject: AMBER: sander errors with atom restraints on ia64

From: Rachel Burdge (rlburdge_at_artsci.wustl.edu)
Date: Thu Feb 17 2005 - 15:46:04 CST

Amber Users,

I have successfully run MD with restrained atoms on an amd64 opteron and
i686 machines. However, when I run the same exact set of files on an
ia64 itanium the restrained atoms are not recognized, but the simulation
continues with no other errors. Has anyone experienced similar problems
using restraints?

Amber was compiled using the 64-bit Intel compilers (configuration
option ia64_ifort):

Intel(R) C++ Itanium(R) Compiler for Itanium(R)-based applications
Version 8.1 Build 20040922 Package ID: l_cc_pc_8.1.022
Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based applications
Version 8.1 Build 20040922 Package ID: l_fc_pc_8.1.019

Thank you-
Rachel Burdge
Washington University in St. Louis

Input file is shown below:

LOADING THE CONSTRAINED ATOMS AS GROUPS
                                                                                                              5. REFERENCE ATOM COORDINATES
  
     Mask :* & !:2855<:20.0; matches 0 atoms

Here is the input file:
                                                                                           MD at 300K, 10ps, 2fs step, shake, npt
 &cntrl
                                                                                             
  nmropt = 0,
  ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
  ntpr = 50, ntwx = 500, ntwv = 0, ntwe = 0,
                                                                                             
                                                                                             
  ntf = 1, ntb = 0,
  cut = 40.0, nsnb = 10,
                                                                                             
  ibelly = 0, ntr = 1, igb = 5, saltcon = 0.2,
  restraint_wt = 10,
  restraintmask = ':* & !:2855<:20.0 & !:WAT',
                                                                                             
                                                                                             
  imin = 0,
  nstlim = 5000,
  nscm = 500,
  t = 0.0, dt = 0.002,
                                                                                             
  temp0 = 50.0, tempi = 50.0,
  ntt = 3,
  gamma_ln = 5,
                                                                                             
  ntp = 0,
                                                                                             
  ntc = 2,
                                                                                             
 &end

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