Hi, guys
Here is one question on the structure minimization for nmode use. the drms from sander minimization with igb=1/2(GB) is about 1.0E-005, but it becomes 5 from nmode ntrun=1, when the structure from sander minimization is used as input coordinate. And this is the case when the warning pops up that "Root-mean-square gradient of input coords is 5.41550205541473
This is greater than the requested maximum: 1.000000000000000E-005". This case happens no matter how big the molecule is, whether it is 44 or 6420. However, when the same molecule with 44 atoms is minimized with nmode ntrun=4, the drms is consistent with that from nmode ntrun=1.
Since ntrun=4 can hardly be used for big molecule with 6420 atoms, I have to use sander for minimization. So can anybody answer my question why the two drms values are so much different? I also tried unformatted file(ntxo=0 and ntx=0), but it dosen't improve much.
Following is my sander minimization input file and nmode ntrun=1 input file.
File for sander minimization
&cntrl
igb=2,
ntf = 1, ntb = 0,
dielc = 1, offset = 0.09, extdiel= 80.0,
cut = 300.0,
scnb = 2.0, scee = 1.2,
imin = 1, maxcyc = 10000,
ncyc = 600,
ntxo=1
&end
nmode input file
&data
maxcyc=100,
ntx = 1,
ntrun = 1, nvect = 0,
dielc = 4.0, idiel = 0,
scnb = 2.0, scee = 1.2
&end
Yongmei Pan
College of Pharmacy, University of Kentucky
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Received on Sun May 14 2006 - 06:07:09 PDT
