AMBER Archive (2008)

Subject: RE: AMBER: minimization

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Oct 30 2008 - 13:48:11 CDT

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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