VMD-L Mailing List
From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Feb 19 2015 - 17:48:43 CST
1) the force field that you are using is parameterized at a certain
temperature. Moving too far away will generate unrealistic results. So use
2) rattle like shake is a constraining algorithm. From what I can recall
it's used for constraining the motion of hydrogens. Is the failure always
always with a hydrogen atom ?? If you are interested only in the unfolding
and not the specifics of the intermediate metastable states which I think
you are not since you have already used implicit solvation, I would
recommend finding a way in which you simulate your system without
hydrogens. Given that they are what is causing the failure in the
Also since i am not an expert wait for someone else to reply, otherwise try
what I said.
Hope that helps.
On Feb 20, 2015 12:00 PM, "Jevgenij Raskatov" <jraskato_at_ucsc.edu> wrote:
> Dear all,
> I am running a high temperature simulation (1500 K, generalized Born
> implicit solvent) in order to unfold a protein, and keep getting the
> following message
> ERROR: Constraint failure in RATTLE algorithm for atom 241!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely; see error messages above.
> I tried raising cutoff and pairlistdiff from the default of 12 and 14 to
> 20 and 24, respectively, but the problem keeps recurring, although the
> failure is listed for a different atom each time. I started from a solution
> structure, and ramped the temperature up gradually. 500K and 1000K both
> worked for 100 ns at 2 fs/step, each, but 1500K became problematic.
> Any advice?
> Dr. Jevgenij A. Raskatov
> Assistant Professor in Chemistry and Biochemistry
> Tel.: +1-831-459-2978
> Department of Chemistry and Biochemistry
> Physical Science Building 356
> 1156 High Street
> Santa Cruz, CA
> 95064 USA