[AMBER] Steered MD using pmemd.cuda ?

From: Marek Maly <marek.maly.ujep.cz>
Date: Thu, 14 Jul 2011 18:51:21 +0200

Hello all,

my colleague asked me if it is possible to do Steered MD using Amber
GPU implementation which means for the moment pmemd.cuda. I didn't
use this technique till now so I tried just simple test with sample input
(page 126 of Amber11 manual) below is the full input. This input was
and simulation was performed without any error but reqested "smd.txt" was
not created
so I am not sure if "ncsu_smd" part of my input was not simply ignored by
although I found the full input info written in *.out file.

Thanks in advance for relevant comments !

    Best wishes,

       Marek Maly

heat ras-raf
   cut=10.0, ntb=2, ntp=1, taup=2.0,
   ntpr=5000, ntwx=5000,
   ntt=3, gamma_ln=2.0,

   output_file = 'smd.txt'
   output_freq = 50
   type = DISTANCE
   i = (5, 9)
   path = (X, 3.0) path_mode = LINES
   harm = (10.0)
   end variable
end ncsu_smd

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Received on Thu Jul 14 2011 - 10:30:02 PDT
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