Re: [AMBER] .mdin file content

From: Richard Owczarzy <>
Date: Mon, 13 Dec 2010 23:28:25 +0000

I think that you set up simulation such a way that the files are manageable and you can analyze results. If you have a Linux box with more memory, VMD will not crash. If you use Mac or Windows, you need smaller files (<2GB).

By the way, you do not have to load all frames to VMD, just load every second or third frame and VMD may not crash. When you open a file and look at left bottom corner of the "Molecule File Browser" of VMD, there is a input for "Stride". Set stride to 2 and VMD will read every second frame. Set it to 3 and VMD will read every third frame.

Richard Owczarzy
Integrated DNA TEchnologies

From: Bozell, Joseph John []
Sent: Monday, December 13, 2010 3:36 PM
Subject: [AMBER] .mdin file content

These may be very basic questions normally answered with "it depends", but I am wondering if the list can point me toward any information regarding rules of thumb for setting some of the more common .mdin file parameters. Some specific questions:

1) With the following .mdin file:


  imin = 0,

  irest = 1,

  ntx = 7,

  ntb = 2,

  pres0 = 1.0,

  ntp = 1,

  taup = 2.0

  cut = 12,

  ntr = 0,

  ntc = 2,

  ntf = 2,

  tempi = 380.0,

  temp0 = 300.0,

  ntt = 3,

  gamma_ln = 1.0,

  nstlim = 1000000, dt = 0.002,

  ntpr = 1000, ntwx = 100, ntwr = 1000


I end up generating an immense .mdcrd file (6.2 GB) that crashes VMD on my MacBook pro after loading about 85% of the generated frames (with the standard Mac error message "VMD 1.8.7 quit unexpectedly"). Is reducing the file size by lowering the number of writes to that file acceptable (i. e., for scrutiny by others) via modifying ntwx to, say, 1000, or 10000? I note that from the manual I could also set ntwprt to limit the .mdcrd file to only the portions of interests. However, I am examining an array of 5 small organics in a water box. Are the atom numbers referred to for setting ntwprt those listed in the first column of the .prepin file? That would not seem to be the case, as there aren't enough atoms to account for all 5 molecules being modeled.

2) The term "production dynamics" gets used frequently…however, the literature reports setting nstlim for "long" runs at anywhere from 2 to 40 nanoseconds. Is there any consensus on what defines a production run?

An understanding of typical baseline parameters for average runs would be a big help in then understanding the types of values more outside of the norm. Any guidance is greatly appreciated.

Joe Bozell

University of Tennessee
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Received on Mon Dec 13 2010 - 15:30:03 PST
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