AMBER Archive (2006)

Subject: Re: AMBER: restraints and constant pressure

From: Joshua (
Date: Fri Sep 15 2006 - 04:09:44 CDT

Dr. Cheatham,

Thank you very much for your reply, this helps a lot. I have two questions:

Just to make sure I am understanding correctly: The scaling process changes the relative positions of separate protein chains, but it does not change the relative positions of the atoms within a given protein chain. Is that correct?

If I need to edit the prmtop file to represent everything as a single chain, how would I go about doing that? If I have already run several simulations using the old prmtop file, is it okay to edit it now, mid-way through the sequence of simulations?

If you could let me know your thoughts on these questions I would really appreciate it. Thanks again for your detailed reply.


 --- On Fri 09/15, Thomas Cheatham < > wrote:
From: Thomas Cheatham [mailto:]
Date: Fri, 15 Sep 2006 00:22:02 -0600 (Mountain Daylight Time)
Subject: Re: AMBER: restraints and constant pressure

> "Using constant pressure with restraints can also cause problems so > initially we will run 20 ps of MD at constant volume."> > I am working with a system where it is really necessary to use > restraints on about one third of the solute. I had planned on using > ntr=1 with a force constant of 10 kcal/mol. Could someone please specify > what the risks are of combining restraints with constant pressure, and > how I can minimize those risks?At issue is that pressure scaling works by shifting (scaling) the relative positions of each molecule (in older versions when NPSCAL=1 or atoms when NPSCAL=0) in the box to increase or decrease the size.To simplify the restraint code, rather than inducing a force (coordinate deviation) every time the simulation coordinates are scaled (relative to the restraint coordinates), it was decided to scale the restraint coordinates as well. This effectively changes the restraint coordinates at each step (every time the coordinates are scaled). Tw!
problems may result:(1) when you restart, and reference previous restraint coordinates (that were not shifted), you will get an initially large restraint energy due to the "shift", and(2) if you are restraining multiple molecules, the relative positions of the molecules will change as the simulation proceeds. Imagine the default case where the density of the water is too low initially, the box has to contract. If you are restraining two molecules, for example the two strands of DNA, as the run continues, the restraint coordinates will shift the molecules closer together which will force your MD coordinates to cause the two strands to get closer. This is undesirable.In the older DNA tutorial, a discussion was present that provided this info; to get around (2), I normally edit the prmtop file to coalesce the first two molecules (i.e. two strands of DNA for example) into a single molecule (and change the pointers to reflect this).To get around (1), I normally use the restrt
file as the refc coordinates for a continuation...So, short summary: if you are restraining a single molecule (like a single protein chain), you likely will not suffer serious artifact and can get away with shifting (as per (1) above) noting that upon restart the restraint energy will be a little higher than expected due to the shifting. As long as the force constant for NTR is not too high (1.0 kcal/mol is often strong enough a restraint), this shift should not lead to integration failure.I hope this helps,--tom-----------------------------------------------------------------------The AMBER Mail ReflectorTo post, send mail to amber_at_scripps.eduTo unsubscribe, send "unsubscribe amber" to

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