RE: AMBER: SHAKE probelm

From: Huang, Hai <>
Date: Tue, 23 Nov 2004 16:01:25 -0600

Hi, Ross,
I have tried any kind of possibilities causing the instability according to your kind answer, however, the problem still remains. Actually, I am running in water with periodic boundaries. I minimize the backbone of my generated molecular first, then water and whole system, finally run molecular dynamics at 300K with dt=0.001fs. The mdin files are just copies of those in DNA tutorial. I am very confused now, do you have any further idea about this problem? One of my collegues suggests that the constraints may help, is that true?

All the best,



From: on behalf of Ross Walker
Sent: Fri 11/19/2004 5:09 PM
Subject: RE: AMBER: SHAKE probelm

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 slowly.
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

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Received on Tue Nov 23 2004 - 22:53:00 PST
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