Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization

From: 张冬冬 <>
Date: Fri, 15 Aug 2014 17:26:33 +0800 (GMT+08:00)

Thanks so much for your reply! With your remind, I've changed the force field to try again.
Actually I'm quite sure about the underlying problem behind the results, which have large RMS, stars form like **** of VDW and EEL in it. I have checked the system structure and found that there are two atoms ( belonging to different residues ) getting very closer (almost sitting on each other) and one near bond is stretched after finishing the minimization step two. My question is why this phenomenon (large RMS, stars form like **** of VDW and EEL) happens once in the beginning of the minimization step two? It is still OK in the end of minimization step one. Also, when I compare these results with those produced using non-polarized FF, no such weird things happen. I wonder where it is the polarized FF that leads to the large nonbond interaction between these atoms. Thank you.

> -----原始邮件-----
> 发件人: "David A Case" <>
> 发送时间: 2014年8月14日 星期四
> 收件人: "AMBER Mailing List" <>
> 抄送:
> 主题: Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization
> On Thu, Aug 14, 2014, 张冬冬 wrote:
> > Recently, I've been working on a job about using a polarized
> > FF(leaprc.ff02) to simulate a protein-nanotube system(model
> > processing is as A00). When I run minimization of step one, mdout
> > results seemed to be fine(A01). When I went to step two, however,
> > I found that the RMS and dipole convergence rms became very
> > large(The mdout file is as below A02. ). With many uncertainties
> > I went on with the minimization of step three, and I shockingly
> > found that the RMS and dipole convergence rms turns out to be too
> > large to see(The mdout file is as below A03)!! I have tried many
> > different combinations of namelists in the $cntrl, leading to the
> > same results. When I turned to the amber tutorials hoping to find
> > some helpful answers but I got nothing related to this. So, could
> > you help me with this? All in all, I hope you can give me some
> > suggestions about using amber polarized FF.
> There is not much to go on here: we don't know how you are describing the
> nanotube, or what behavior you expect. The two pretty obvious caclulations to
> try are these:
> 1. Do a calcuation of just the protein in ff02 (You should use the ".R1"
> version, e.g. "source oldff/leaprc.ff02pol.r1". I don't know where you got
> leaprc.ff02 from, perhaps an old version of Amber? Note that the "oldff"
> designation means that these force field is no longer supported or
> recommended, and is only provided if comparisons to old simulations are
> needed.) See if a simple system (perhaps even a peptide) works the way you
> hope it will. This will help eliminate possible problems with the nanotube
> part.
> 2. Do a calculation with a non-polarizable potential. This will help make
> sure that the system is working OK (or not) in the absence of polarizability.
> Upgrading to the current version of Amber will make it much easier for people
> on the list to provide help.
> ....dac
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Received on Fri Aug 15 2014 - 02:30:02 PDT
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