AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1?

From: Pan, Yongmei <>
Date: Thu, 11 May 2006 10:13:02 -0400

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



  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,




nmode input file



  ntx = 1,

  ntrun = 1, nvect = 0,

  dielc = 4.0, idiel = 0,

  scnb = 2.0, scee = 1.2



Yongmei Pan

College of Pharmacy, University of Kentucky

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun May 14 2006 - 06:07:09 PDT
Custom Search