AMBER Archive (2009)

Subject: [AMBER] difference in temperature

From: Naser Alijabbari (na3m_at_virginia.edu)
Date: Tue May 05 2009 - 19:02:28 CDT

Hello,

Below are the some of the eigenvectors for the second eigenfrequency from a
MD simulation of E. coli’s thioredoxin. This is using AMBER10 running on Duo
Core EM64T processor (serial simulation), with explicit solvation (8
angstrom water shell, and 10 angstrom cutoff). There is very little
difference between eigenvalues and eigenvectors when the temperature is 293K
but there is a noticeable difference when 300K is used. I have tried this
experiment with a larger molecule with the same results. I was wondering if
this is to be expected. Should 7 K make a large difference?

* *

*293 K*

*ASCII*

2 3.51672

    0.00249 0.02162 0.00516 -0.00790 0.02538 -0.00174
0.00776

    0.00961 0.00521 0.00855 0.03155 0.01340 0.00107
0.01906

…

* *

*Binary/netcdf*

2 3.51671

   -0.00249 -0.02162 -0.00515 0.00790 -0.02538 0.00173
-0.00776

   -0.00961 -0.00521 -0.00855 -0.03155 -0.01340 -0.00107
-0.01906

…

 *300 K*

*ASCII*

    2 1.27596

    0.00121 0.00935 0.00468 0.00018 0.00926 0.00344
0.00259

    0.00776 0.00708 0.00189 0.01273 0.00539 -0.00028
0.00691

...

*Binary/netcdf*

    2 3.22849

   -0.00081 -0.01854 -0.00147 0.00709 -0.00925 0.00822
-0.01803

   -0.01153 -0.01168 0.00293 -0.03840 -0.00695 0.00715
-0.01343

…

These are the input files used for the production runs that produced the
following eigenvalues and eigenvectors.

*ASCII input file*

&cntrl

  imin = 0, irest = 1, ntx = 5,

  ntb = 1,

  cut = 10, ntr = 0,

  ntc = 2, ntf = 2, tol=.000001,

  tempi = 293.0, temp0 = 293.0, (these are 300K for 300K simulations)

  ntt = 0, nscm=0,

  nstlim = 95000, dt = 0.001,

  ntpr = 100, ntwx = 50, ntwr = 1000,

&end

&ewald

   ew_type=0, dsum_tol=0.00001, skinnb=3,

 &end

*Binary/netcdf input file*

&cntrl

  imin = 0, irest = 1, ntx = 5,

  ntb = 1,

  cut = 10, ntr = 0,

  ntc = 2, ntf = 2, tol=.000001,

  tempi = 293.0, temp0 = 293.0, (these are 300K for 300K simulations)

  ntt = 0, nscm=0,

  nstlim = 95000, dt = 0.001,

  ntpr = 100, ntwx = 50, ntwr = 1000, ioutfm=1,

&end

&ewald

   ew_type=0, dsum_tol=0.00001, skinnb=3,

 &end
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