AMBER Archive (2002)

Subject: Re: Energy problem during dynamics with amber 7

From: David Case (case_at_scripps.edu)
Date: Wed May 15 2002 - 12:29:55 CDT

On Wed, May 15, 2002, Florence CASSET wrote:
>
> Now with Amber7 I'm using the following md0.in parameter file:
>
> MD0 Peptide BoxWater
> &cntrl
> imin = 0, nmropt = 1,
> ntx = 1, irest=0,
> ntxo = 1, ntpr = 1000, ntwx = 1000, ntwe = 1000, ntwprt = 388,
> iwrap=1,
> ntf = 1, ntb = 2, cut = 12.0, nsnb = 10, scee = 1.2,
> ibelly = 0, ntr = 0,
> nstlim = 200000, nscm=1000,
> t = 0, dt = 0.001,tautp = 0.2,
> temp0 = 300.0, tempi = 10.0, ntt = 1, vlimit = 20.0,
> ntp = 1, pres0 = 1.0, comp = 44.6, taup = 0.2, npscal = 1,
> ntc = 1,
> &end
> #Heating
> &wt type='TEMP0', istep1=1, istep2=20000,
> value1=10.0, value2=300.0, &end
> &wt type='TEMP0', istep1=20001, istep2=200000,
> value1=300.0, value2=300.0, &end
> &wt type='END' &end
> &rst iat=0 &end
>
> In this case, with amber7, during the dynamics the energy increased during
> the heating period like previously and then decreased progressively during
> the rest of the dynamics, the decreasing is higher during the 100ps
> following the heating period. I verified the temperature and it is constant
> during the all dynamics after 20ps.

>
> Does someone has observed this problem already,...

It's not clear what the problem is: how much does the total energy change
over 200 psec? If you run for another 200 ps, do things continue to change?
Do the volume and pressure seem OK?

The only thing about your input file that strikes me as unusual is the 12
Ang cutoff: this is overkill, and 8 Ang. should be large enough.

In amber 4.1, I think the default behavior was a non-PME calculation,
whereas by version 7 the default is to use PME. So you are running a very
different type of simulation now than with the earlier code, and some of the
behavior may be different.

Also note that not using SHAKE for explicit water simulations (i.e. ntc=1
rather than 2) means that the water model is not TIP3 (which requires
SHAKE), and may lead to problems; however, this is not obviously related to
what you report.

A good check is (after equilibration) to run some NVE dynamics (ntb=1,
ntp=0, ntt=0) and check the conservation of total energy. If this is not
pretty well conserved, there may be some hidden problems.

...hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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