AMBER Archive (2002)

Subject: Re: Strange MD simulation results with GB solvation at high temp.

From: Soonmin Jang (sjang_at_protege.snu.ac.kr)
Date: Tue Sep 10 2002 - 10:56:53 CDT

Thank you for the reply.
I forgot to mention that I am using Amber7. As I know it automatically
removes translational and rotational motion in default setting.
That is also the what the "mdout" file indicate.
I don't see any overall rotational/translational motion when I watched the
MD movie.
So, I am sure it is not the problem of rotational/translational motion.

Thank you again,

Soonmin

On Tue, 10 Sep 2002, Carlos Simmerling wrote:

> I'm not sure if this is the cause of the problem, but you might
> want to make sure you are removing center of mass rotation
> and translation.
>
> ----- Original Message -----
> From: "Soonmin Jang" <sjang_at_protege.snu.ac.kr>
> To: <amber_at_heimdal.compchem.ucsf.edu>
> Sent: Tuesday, September 10, 2002 6:09 AM
> Subject: Strange MD simulation results with GB solvation at high temp.
>
>
> > Hello,
> >
> > I posted this mail previously but somehow it seems it is not delivered
> > correctly. So, here I post it again.
> >
> > I am running MD with GB solvation (generalied Born). The system is very
> simple.
> > It is Met-Enkephlain { ACE TYR GLY GLY PHE MET NME }.
> > It runs OK up to several nano seconds. But it shows very strange behavior
> > after several naosecond (about 3 ns for in this case).
> > There begin to appear large temperature and energy fluctuation and the
> > energy distribution is NOT Boltzman anymore after this point.
> >
> > Here is the temperature profile as time step. (30000 corresponds to 3.0
> ns).
> >
> > 1000
> ++-------+--------+-------+--------+--------+--------+-------+-------++
> > + + + + + +
> +'bb.dat'******* +
> > | * ** *** ****
> |
> > 900 ++ ********
> *****++
> > |
> ************** |
> > |
> ************** |
> > 800 ++
> ***************++
> > | ** * * * *
> **************** |
> > ************** **** *
> *********************************************** |
> > 700
> *********************************************************************++
> >
> ********************************************************************* |
> > 600
> *********************************************************************++
> >
> ********************************************************************* |
> >
> ********************************************************************* |
> > 500
> *********************************************************************++
> > | * *** * * * *** * ******** * * * *
> ******************* |
> > | * *
> *************** |
> > 400 ++
> **************++
> > | *************
> |
> > + + + + + + + *+
> +
> > 300
> ++-------+--------+-------+--------+--------+--------+-------+-------++
> > 0 5000 10000 15000 20000 25000 30000 35000
> 40000
> >
> >
> > Ans here is the run script I used
> >
> > &cntrl
> > ntb=0, igb=1, ig=17436,
> > imin=0, irest=0, ntx=1, tempi=300.0, ntt=1, temp0=604.0, tautp=0.5,
> > nstlim=4000000, dt=0.001,
> > ntwe=100, ntwx=500, ntpr=5000,
> > &end
> >
> > Any comments will be appreciated.
> > Thank you.
> >
> > Soonmin
> >
> >
> >
> 

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