AMBER Archive (2006)

Subject: RE: AMBER: SHAKE problem after minimization

From: Hayden Eastwood (s0237717_at_sms.ed.ac.uk)
Date: Wed Nov 22 2006 - 14:33:17 CST

Dear Rachel

According to the information you give, the force constant for HD-HD-DH is 0.
Is this right? If HD is the dummy atom, should this not be the force
constant that you define as being 0? I'm not really familiar with dummy
atoms I'm afraid so I might not be the right person to advise you on this
aspect of your problem. Furthermore it's difficult for me to advise you on
whether or not you need to alter the force constants for both HD-DH-HD and
HD-HD-DH because I haven't seen the structure of the molecule you're
examining and I don't know what you're trying to investigate.

However, this is how I treated the problem:

1. I ran an MD simulation that outputted trajectory files at every 1ps time
step. This proecess allowed me to view which of the particles "descended"
into one another.
2. Once I identified the culprit atoms, I identified the corresponding
culpret force constant and tweaked this manually until I obtained stable
dynamics.

If that sounds like hard work, you could just try modifying 1 or other (or
both) of the force constants by increments until stable dynamics are
observed (However, I'd recommend against the easy fix unless you really
understand the system well and are sure that such alterations won't
undermine the basis of your simulation).

I hope that helps!

Hayden

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Rachel
Sent: 22 November 2006 19:37
To: amber_at_scripps.edu
Subject: Re: AMBER: SHAKE problem after minimization

Dear Hayden,
 
Thanks for your reply, yes, i do have some home-made residues, which are
hydrogen molecules, i used a three-atom model, with two hydrogen atoms (type
HD) and one dummy atom in-between the two hydrogen atoms (type DH), and the
charge of both HD are - 0.475, and +0.95 on DH, and the following is the
.frcmod file i used for this residue:
######################################
# H2 molecule parameters

MASS
HD 1.008
DH 1.008

BOND
HD-DH 150.00 0.742
HD-HD 150.0 1.484

ANGLE
HD-DH-HD 500.0 180.0
HD-HD-DH 0.000 180.0

DIHEDRAL

IMPROPER

NONBON
HD 0.000 0.000
DH 2.920 0.2722
#########################################
 
As you can seen, I assumed the mass of DH is the same as HD (which is not
correct). And as i wanted to keep these three atoms in the same line, so i
added one extra bond between two HD atoms as suggested by Yong. So shall i
increase the force constant for HD-DH-HD or HD-HD-DH or both?
 
Thanks very much!
Best regards,
Rachel
 

On 11/22/06, Hayden Eastwood <s0237717_at_sms.ed.ac.uk> wrote:

        Dear Rachel
        
        I have had similar problems to you when running dynamics with
home-made
        residues. There is a defect in the amber force field with regards to

        treating various highly charged groups in bonding proximity. If you
have a
        home made molecule then I have the following question:
        
        Do you have any Phosphate-oxygen bonding neighbours with very large
opposite
        charges? Or any other bonding pairs with huge charge differences? If
you do,
        this could be the cause of the crash. AMBER assumes that the bond
angle
        barrier is large enough to prevent neighbouring connected atoms from

        collapsing into one another. However, in some situations (i.e. with
        oppositely highly-charged atom pairs) this barrier is overcome and
the atoms
        are pulled down a pairwise electrostatic interaction slope until
they
        overlap and cause your energy to go crazy.
        
        The cure: artificially increase the bond angle force constants in
the force
        field parameter file and this should prevent them running into each
other
        (although the dynamical behaviour of some of the affected groups
will of
        course be "stiffer").
        
        I don't really understand the nuts and bolts of why the atoms
descend into
        one another given that there should be van der waals terms that
prevent
        this...Mike Crowley personally explained it to me once and whilst it
made
        sense at the time the explanation now seems a little fuzzy!
        
        If it's not a home made residue with the above mentioned
characteristics
        then I'd suggest you follow Ross's advice.
        
        Best
        
        Hayden
        
        
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