Re: [AMBER] Why RMSD goes fast to 5 angstrom?

From: Aron Broom <broomsday.gmail.com>
Date: Tue, 17 Apr 2012 22:40:58 -0400

First, are you calculating the RMSD with a method that allows you to first
align the backbone? If not, your RMSD will incorporate deviations due to
translations and rotations, although I suspect that is not the case here.

This simply seems like your crystal structure is not an accurate model for
the solution structure, or at least, not an accurate model for the solution
structure as defined by the forcefield you are using. Which forcefield are
you using? Which water model? Are you certain that your parameters are
appropriate for those models?

Also, if you just watch the trajectory (in VMD for instance) how does it
look? An RMSD of 5A could easily be caused by a single strand or loop or
something that is not behaving in a well structured manner. Moreover, it
may be that in reality it doesn't behave that way, but the dense packing in
the crystal, and low temperature of X-ray diffraction have made that region
appear rigid.

I think there is a tutorial for VMD, that you might have to access through
the NAMD website, that will guide you through assigning RMSDs on a
per-residue basis. You could do that and then colour the structure
accordingly and see which regions are contributing to the high RMSD.

Finally, depending on the size of your protein and the quality of the
crystal (1.9 angstroms resolution is decent, but not amazing) it simply
might take more than 11ns to reach a stable structure from the possibly
inaccurate starting point.

~Aron

On Tue, Apr 17, 2012 at 10:26 PM, Shulin Zhuang <shulin.zhuang.gmail.com>wrote:

> Dear All,
>
> I have routinely performed a 11 ns MD simulation in NPT ensemble based on
> X-ray crystal structure with a resolution of 1.87 angstrom . After the RMSD
> analysis, I found that the C alpha RMSD is continiously increasing and
> finally is is up to *5 *. The averaged RMSD for the* 0-1ns* simulation,
> *
> 1-6ns* simulation, *6-11ns* simulation is *2.3** , 2.86 , 3.89
> ,*respectively. Attached
> is the RMSD figures.* It seems abnormal* and could you tell me where is the
> problem.
>
> The simulatioin input files were listed as following:
> *
> Minimization step 1 input:*
>
> restrained mimimization
>
> &cntrl
>
> imin=1, maxcyc=1000, ncyc=500, cut=10.0, ntb=1,
>
> ntr=1, restraintmask='(:268) & (!.H=)', restraint_wt=10.0
>
> # here 268 is the ligand. In this step, the ligand and non-hydrogen part of
> the system were restrained.
>
> /
>
> *Minimization step 2 input:*
>
> restrained mimimization
>
> &cntrl
>
> imin=1,maxcyc=1000, ncyc=500, cut=10.0, ntb=1, ntr=0,
>
> /
>
> *Heating stage input:*
>
> restrained heating process
>
> &cntrl
>
> imin=0, irest = 0, ntx = 1, ntb = 1, ntr = 1, ntc= 2, tempi = 0.0,
> temp0 = 300.0,
>
> ntt = 3, gamma_ln = 1.0, nstlim = 25000, dt = 0.002, ntpr = 100, ntwx
> = 500, ntwr = 500,
>
> cut=10.0, restraintmask='(:268) & (!.H=)', restraint_wt=5.0,
>
> ******
>
> */*
>
> *
> *
>
> *1ns equilibration input:*
>
> &cntrl
>
> ntx =7, ntr = 0, irest = 1, imin = 0, nrespa = 1, ntb =2, ntp=1,
>
> tempi =300.0, temp0 =300.0,cut=10.0, nstlim =500000, dt= 0.002, ntpr=200,
>
> ntc=2, ntf=2, taup = 2, pres0 = 1.0, ntwr=500, ntwx=500, ntt=3,
> gamma_ln=1.0,
>
> *5ns equilibration input:*
>
> &cntrl
>
> ntx =5, ntr = 0, irest = 1, imin = 0, nrespa = 1, ntb =2, ntp=1, tempi
> =300.0,
>
> temp0 =300.0,cut=10.0, nstlim =2500000, dt= 0.002, ntpr=200, ntc=2,
> ntf=2, taup = 2, pres0 = 1.0,
>
> ntwr=500, ntwx=500, ntt=3, gamma_ln=1.0,
>
> *5ns equilibration input:*
> &cntrl
> ntx =5, ntr = 0, irest = 1, imin = 0, nrespa = 1, ntb =2, ntp=1,
> tempi =300.0, temp0 =300.0,cut=10.0, nstlim =2500000, dt= 0.002,
> ntpr=200,
> ntc=2, ntf=2, taup = 2, pres0 = 1.0, ntwr=500, ntwx=500, ntt=3,
> gamma_ln=1.0,
> /
>
>
> Much appreciated to your help!
>
> Shulin
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>


-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Apr 17 2012 - 20:00:05 PDT
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