AMBER Archive (2005)

Subject: Re: AMBER: minimization stuck problem

From: blakrose_at_gazeta.pl
Date: Sat Aug 20 2005 - 16:11:54 CDT

Dear Ross!
 
Thanks for anwsering.
I have maked cut bigger (15) and EEL is now very big. I hope it's
not too big:
My input now is:
 &cntrl
    imin=1, maxcyc=500, ncyc=100,
    scee=1.2, cut=15., ntb=2, ntp=2,
    dielc=1.0,
    nsnb=20,
    ntpr=5,
    ntr=0,
 &end
 &ewald
    use_pme=0,
    nbflag=0,
    netfrc=0,
    eedmeth=1,
 &end
 
Some of oututs line:
  NSTEP ENERGY RMS GMAX NAME
NUMBER
      1 -8.6476E+05 6.4681E+01 2.4709E+02 O
37174
 
 BOND = 196.5343 ANGLE = 819.6722 DIHED =
2463.2979
 VDWAALS = 15051.3535 EEL = -894109.1116 HBOND =
0.0000
 1-4 VDW = 898.4235 1-4 EEL = 9921.4357 RESTRAINT =
0.0000
 
 
  NSTEP ENERGY RMS GMAX NAME
NUMBER
     40 -8.6709E+05 6.4349E+01 2.4613E+02 O
37174
 
 BOND = 205.7242 ANGLE = 820.3092 DIHED =
2463.7349
 VDWAALS = 15054.8365 EEL = -896452.7636 HBOND =
0.0000
 1-4 VDW = 898.4925 1-4 EEL = 9923.3598 RESTRAINT =
0.0000
 
 
Is there anything strange that you see in my output or input?
Thanks for all
Pawel G.
 
 
> &cntrl
> imin=1, maxcyc=5000, ncyc=250,
> scee=1.2, cut=10., ntb=1,
> dielc=1.0,
> nsnb=20,
> ntpr=5,
> ntr=0,
> &end
> &ewald
> use_pme=0,
> nbflag=0,
> netfrc=0,
> eedmeth=1,
> &end
 
Is there a reason you are not using pme? Note, without Ewald
treatment of
the long range electrostatics the cutoff needs to be much larger.
A value of
10.0 is very small for this type of calculation. You should
ideally use a
value of around 16.0 or so otherwise you are truncating your
electrostatics
far too early.
 
All the best
Ross
 
/\
\/
|\oss Walker
 
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |
 
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