AMBER Archive (2005)

Subject: AMBER: minimization stuck problem

From: blakrose_at_gazeta.pl
Date: Mon Aug 22 2005 - 10:17:29 CDT

Hi,
 
It's like that:
There is no particular reason why I am not using PME.
Now I would like to note some things.
In my 'Case' :) the is strange things. I used PME with cut=10 and
the EEL from not using PME with CUT=15 are far from each other (
in the beginning and in the end.) It is like 4 times bigger
without PME.
 
 
When I started calculations with input:
 
 &cntrl
    imin=1, maxcyc=200, ncyc=50,
    scee=1.2, cut=10., ntb=2, ntp=2,
    ntc=2, ntf=2,
    dielc=1.0,
    nsnb=20,
    ntpr=5,
    ntr=0,
 &end
 &ewald
  netfrc=0,
 &end
 
and after 150 steps:
 
     .... RESTARTED DUE TO LINMIN FAILURE ...
 
 
                    FINAL RESULTS
 
 
 
   NSTEP ENERGY RMS GMAX NAME
NUMBER
    154 -1.5809E+05 1.3968E+01 4.3722E+01 O
18931
 
 BOND = 146.4009 ANGLE = 808.6642 DIHED =
2455.6066
 VDWAALS = 8926.9064 EEL = -181228.0107 HBOND =
0.0000
 1-4 VDW = 888.0213 1-4 EEL = 9909.1558 RESTRAINT =
0.0000
 
     ***** REPEATED LINMIN FAILURE *****
 
MINIMIZATION STOPPED!!!
 
I know. You will say it is all right. I wanted to see if it is all
right turning shake off. I was thinking that if I turn off shake
I will not get LINMIN F. I get this:
                   FINAL RESULTS
 
 
 
   NSTEP ENERGY RMS GMAX NAME
NUMBER
    200 -1.0179E+05 2.5166E+01 6.8313E+03 HD22
2190
 
 BOND = 95385.8514 ANGLE = 2652.0349 DIHED =
2473.3115
 VDWAALS = 18802.6777 EEL = -232071.8882 HBOND =
0.0000
 1-4 VDW = 1073.8488 1-4 EEL = 9896.9633 RESTRAINT =
0.0000
 
ENERGY is bigger than without shake. I guess it is all right.
Bond energy is bigger than without shake - is it strange?
 
NEXT I did a longer minimisation to see if RMS/GMAX is gatting
lower or not.
 
Input:
 &cntrl
    imin=1, maxcyc=2000, ncyc=500,
    scee=1.2, cut=10., ntb=2, ntp=2,
    dielc=1.0,
    nsnb=20,
    ntpr=5,
    ntr=0,
 &end
 &ewald
  netfrc=0,
 &end
 
 
Output:
   NSTEP ENERGY RMS GMAX NAME
NUMBER
    500 -1.4446E+08 6.5739E+11 1.4574E+14 H
4153
 
 BOND = 10599.5597 ANGLE = 875.0340 DIHED =
2434.6069
 VDWAALS = 16512.0082 EEL = -227239.9604 HBOND =
0.0000
 1-4 VDW = 885.5633 1-4 EEL = ************* RESTRAINT =
0.0000
 
 
   NSTEP ENERGY RMS GMAX NAME
NUMBER
    505 2.5924E+20 2.6173E+09 4.2118E+11 O1G
4154
 
 BOND = ************* ANGLE = 807.7721 DIHED =
2432.8698
 VDWAALS = 16767.0706 EEL = ************* HBOND =
0.0000
 1-4 VDW = 885.6549 1-4 EEL = 10036.1583 RESTRAINT =
0.0000
 
 
   NSTEP ENERGY RMS GMAX NAME
NUMBER
    510 4.0046E+15 1.0296E+07 1.6560E+09 O1G
4154
 
 BOND = ************* ANGLE = 807.9387 DIHED =
2432.8896
 VDWAALS = 35631.2851 EEL = ************* HBOND =
0.0000
 1-4 VDW = 885.6612 1-4 EEL = 10036.1268 RESTRAINT =
0.0000
 
I don't know what is happening. Please help me.
I have visualise structure and looked at atoms closley but there
is nothing strange.
 
Pawel
 
 
 
 

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