Re: [AMBER] problem with the energetics of the system

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Fri, 18 Jun 2010 09:47:00 -0700


> I heat the system step by step from 0 to 308 K
> for about 20 ps, after minimizition.

Stepwise warming is good. How about NVT vs. NPT?
If you send your mdin files, we can check more
in detail. 20ps seems a little short for a big
system. Did you graph e.g. density and rms?

> the below message came after 48 ns.
> also my system is a dimer protein with one ligand.
I assume that's 48 ps?
In such cases the ligand parameterization is the main suspect,
but my impression is that usually it happens sooner if this is
the case. Another possibility that occurs to me is that you might
be restarting with the wrong restrt file or mdin.

> vlimit exceeded for step 0; vmax = 388.4665
> vlimit exceeded for step 1; vmax = 399.4700
> vlimit exceeded for step 2; vmax = 387.9217
> vlimit exceeded for step 3; vmax = 352.8459
> vlimit exceeded for step 4; vmax = 32817.3873
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 3 302 606 607
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.

I think atoms 606, 607 are the problem here. One thing you could try
is to save every step to mdcrd and watch what happens in a dynamics
viewer like VMD.


AMBER mailing list
Received on Fri Jun 18 2010 - 10:00:03 PDT
Custom Search