AMBER Archive (2004)

Subject: AMBER: NTF

From: L Jin (s0344557_at_sms.ed.ac.uk)
Date: Fri Jan 16 2004 - 05:15:16 CST

Dear all,

I am trying to run MD with ntf=6 to constrain some interactions within the
molecule. But when I set ntc=3, the MD clashed with the following message. So I
think it might be the ntc & ntf are not proper. When ntc=ntf=3 it is OK. But I
want to constrain some other bonds and angles. Then how should I set the value?

  Here is the input file:

MD in-vacuo, 999.0 angstrom cutoff
 &cntrl
   igb = 0, ntb = 0, ntpr = 100, ntwx = 100, ntwe = 100,
                                                                               
   cut = 999.0, ntc = 3, ntf = 6,
                                                                               
   tempi = 300.0, temp0 = 300.0, ntt = 1, tautp = 0.5,
                                                                               
   imin = 0,
   nstlim = 1000000, dt = 0.001,
                                                                               
 &end

  Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 2 20 39 40

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.
 

What is the deeper problem here? Is it serious? How can I modify it?

And I want to keep running the MD with the lowest energy frame so I need its
restrt file to use the crd & velocity. But I cannot get the correct restrt file
with carnal and ptraj. Thanks a lot in advace.

restrt file from carnal:no velosity

CARNAL temporary title
  45
   7.0250000 0.5290000 -0.2430000 6.9230000 0.4630000 0.7100000
   5.7850000 0.0740000 -0.8060000 4.9920000 0.7540000 -0.4950000
   5.4860000 -1.3280000 -0.3090000 6.3570000 -1.9790000 -0.3760000
   5.1340000 -1.2690000 1.1170000 4.9350000 -2.1800000 1.3450000
   5.8330000 0.0530000 -2.3450000 6.7030000 -0.4940000 -2.7100000
   5.9080000 1.3410000 -2.8150000 6.5830000 1.7400000 -2.2610000
   4.5670000 -0.6140000 -2.9090000 3.6990000 -0.0770000 -2.5280000
   4.5330000 -0.7140000 -4.4320000 4.8390000 0.1580000 -5.0100000
   5.1830000 -1.5020000 -4.8130000 3.2140000 -1.0300000 -4.7870000
   2.9160000 -1.7690000 -4.2520000 4.4220000 -1.9590000 -2.4050000
   4.3000000 -1.9570000 -0.9950000 3.3950000 -1.3770000 -0.8150000
   3.9900000 -3.2860000 -0.6460000 5.0260000 -4.3570000 -0.4570000
   6.0330000 -3.9460000 -0.5310000 4.8100000 -5.1680000 0.8440000
   5.5360000 -5.9780000 0.9080000 5.0660000 -4.2460000 1.9530000
   4.9160000 -4.7550000 2.7530000 3.3920000 -5.7070000 0.8220000
   2.6710000 -4.8900000 0.7780000 3.1060000 -6.5270000 2.0090000
   2.1550000 -6.6290000 2.0910000 3.1370000 -6.6190000 -0.4050000
   3.7500000 -7.4980000 -0.2070000 1.6540000 -7.1040000 -0.5230000
   1.6830000 -7.8320000 -1.3330000 1.3190000 -7.5780000 0.3990000
   0.6160000 -6.1420000 -0.8360000 1.0560000 -5.4650000 -1.3560000
   3.5250000 -5.9020000 -1.5850000 4.8840000 -5.4850000 -1.5030000
   5.5760000 -6.2810000 -1.2250000 5.1820000 -5.0520000 -2.8120000
   4.6010000 -4.3230000 -3.0410000

restrt file from ptraj:

restrt file generated by ptraj
   45
   7.0250001 0.5290000 -0.2430000 6.9229999 0.4630000 0.7100000
   5.7849998 0.0740000 -0.8060000 4.9920001 0.7540000 -0.4950000
   5.4860001 -1.3279999 -0.3090000 6.3569999 -1.9790000 -0.3760000
   5.1339998 -1.2690001 1.1170000 4.9349999 -2.1800001 1.3450000
   5.8330002 0.0530000 -2.3450000 6.7030001 -0.4940000 -2.7100000
   5.9080000 1.3410000 -2.8150001 6.5830002 1.7400000 -2.2609999
   4.5669999 -0.6140000 -2.9089999 3.6989999 -0.0770000 -2.5280001
   4.5330000 -0.7140000 -4.4320002 4.8390002 0.1580000 -5.0100002
   5.1830001 -1.5020000 -4.8130002 3.2140000 -1.0300000 -4.7870002
   2.9159999 -1.7690001 -4.2519999 4.4219999 -1.9590000 -2.4050000
   4.3000002 -1.9570000 -0.9950000 3.3950000 -1.3770000 -0.8150000
   3.9900000 -3.2860000 -0.6460000 5.0260000 -4.3569999 -0.4570000
   6.0330000 -3.9460001 -0.5310000 4.8099999 -5.1680002 0.8440000
   5.5359998 -5.9780002 0.9080000 5.0660000 -4.2459998 1.9529999
   4.9159999 -4.7550001 2.7530000 3.3920000 -5.7069998 0.8220000
   2.6710000 -4.8899999 0.7780000 3.1059999 -6.5270000 2.0090001
   2.1550000 -6.6290002 2.0910001 3.1370001 -6.6190000 -0.4050000
   3.7500000 -7.4980001 -0.2070000 1.6540000 -7.1040001 -0.5230000
   1.6830000 -7.8319998 -1.3329999 1.3190000 -7.5780001 0.3990000
   0.6160000 -6.1420002 -0.8360000 1.0560000 -5.4650002 -1.3559999
   3.5250001 -5.9020000 -1.5850000 4.8839998 -5.4850001 -1.5030000
   5.5760002 -6.2810001 -1.2250000 5.1820002 -5.0520000 -2.8120000
   4.6009998 -4.3230000 -3.0409999
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
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   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
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   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000
   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000

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