AMBER Archive (2008)

Subject: AMBER: minimization

From: Jacopo Sgrignani (jacopo.sgrignani_at_unifi.it)
Date: Fri Oct 31 2008 - 03:52:12 CDT

Thank Ross,

this is my input
Minimization
 &cntrl
  imin=1, maxcyc=20000, NCYC=5000
  ntpr=500, scee=1.2, cut=10.0, drms=0.001,
 &end
END
END

and this is the output of my minimisation: the atom with the largest
force is in a water molecule, this is very strange.
I have problems to understand the reasons for the strange value of the
electrostatic energy.

  NSTEP ENERGY RMS GMAX NAME NUMBER
  1500 -6.1989E+07 9.5130E+10 3.4646E+13 O 39074

 BOND = 621297.4559 ANGLE = 12297.8211 DIHED = 9920.4195
 VDWAALS = 1088705.3404 EEL = ************* HBOND = 0.0000
 1-4 VDW = 4105.3057 1-4 EEL = 43532.3673 RESTRAINT = 0.0000

    .... RESTARTED DUE TO LINMIN FAILURE ...

The atom with the largest force is in a water molecule, this is very strange.
I have problems to understand the reasons for the strange value of the
electrostatic energy.

On Thu, Oct 30, 2008 at 7:48 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> Hi Jacopo,
>
> It's very hard to help without knowing what you are doing seeing some of the
> output etc. I suspect that your initial structure is highly strained and
> this is causing problems during minimization. Look to see if any of the
> energy terms are excessively large suggesting long bonds, atoms sitting on
> top of each other etc.
>
> You should also look at the line showing the total energy and GMAX for step
> 1 since this will indicate the atom with the largest force on it and then
> you can visualize that and see if the structure looks bad around this atom.
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
>> Of Jacopo Sgrignani
>> Sent: Thursday, October 30, 2008 11:03 AM
>> To: amber_at_scripps.edu
>> Subject: AMBER: minimization
>>
>> Hi
>> I'm trying to minimize some snapshots extracted (using ptraj) from an
>> MD simulation but i have a problem. Actually the rmsd value don't go
>> down but it has an increment during the minimization. Moreover during
>> the minimization the electrostatic energy or vdw values become very
>> high.
>> Does Anybody have any advices to overcome this problem?
>>
>> Thanks
>>
>> Jacopo
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