RE: AMBER: SHAKE probelm

From: Ross Walker <>
Date: Fri, 19 Nov 2004 15:09:05 -0800

It could be all sorts of things causing your instability. Are you running in
gas phase? Most systems will be unstable in gas phase. Ideally you want to
run in water with periodic boundaries.
If this is a system you built yourself you are almost certainly going to
have to carry out very careful minimisation and equilibration on the system.
See the amber tutorials for some examples (E.g. DNA).
You will probably need to do minimisation on just your water, followed by
minimisation on the whole system. You will then need to run MD with
restraints on your system and "slowly" raise the temperature (at constant
volume) then relax the restraints on your system and allow it to equilibrate
at 300K (constant volume) - then switch to constant pressure.
Note, if you system is very unstable, as is often the case with hand built
structures, you may need to do many stages starting the MD initially with a
very small time step (say 0.1fs) to allow the system to re-arrange very
I hope this helps.
All the best
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |



From: [] On Behalf Of
Huang, Hai
Sent: 19 November 2004 14:57
Subject: RE: AMBER: SHAKE probelm

Hi, Ross,

Thank you for your helpful suggestions, I run 1,000 frames as you adviced
and viewed the result with VMD. It seems that the system is unstable, so
which reason may cause the unstability? Actually, before running MD, I have
carried out a short time minimization. BTW, I checked my starting structure
again, I didn't find any atoms too close.


-----Original Message-----
From: on behalf of Ross Walker
Sent: Fri 11/19/2004 11:35 AM
Subject: RE: AMBER: SHAKE probelm

Your system is probably unstable. With shake off have you looked carefully
at the structure over time (mdcrd)? What about the energies and the

Try running 1,000 frames or so with ntwx set to 1. Then visualise it in
something like VMD, the problem should be obvious, you either have two atoms
close together or your system is unstable. I trust you have carried out
extensive minimisation on your system before starting MD.

All the best


From: [] On Behalf Of
Huang, Hai
Sent: 19 November 2004 08:25
Subject: AMBER: SHAKE probelm

Hi, all,

I am a new user of AMBER. I generated a crosslink of oligonucleotide and
peptide with amber7. I try to simulate its structrure with molecular
dynamics, it works well with SHAKE off (ntc=1, ntf=1), however, when SHAKE
is turned on (ntc=2, ntf=2), the running crashs rapidly and error message
     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 11 7 12 13

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

I have carefully checked the structure. LEAP doesn't report any error or
warning. Does anyone have any idea about this problem? Thank you.

Hai Huang

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Nov 19 2004 - 23:53:01 PST
Custom Search