AMBER Archive (2001)

Subject: Re: problem in a short MD with protein fixed

From: Michael G Cooney (chemgc_at_panther.Gsu.EDU)
Date: Wed Oct 17 2001 - 13:52:30 CDT

Dear Dr. Wang,

I see two possible problems: first, your time step (dt) is too large at
0.02 ps (this is 20 fs, the normal value being 2 fs or .002 ps with
shake); second, the restraint of 2000 kcal/mol seems large also. The error
is a SHAKE error as far as I can tell, so lowering dt to .002 will
probably fix it. Hope this helps.

Sincerely,

Michael G. Cooney, Ph.D.
Dept. of Chemistry
Georgia State University
Atlanta, GA 30303

On Tue, 16 Oct 2001, dwang wrote:

> I am trying to do a short MD with holding protein fixed. But it gave me
> the following error message,
>
> ---------------------------------------------------
> Total number of mask terms = 70195
> Total number of mask terms = 140390
> | Total Ewald setup time = 0.17934799
> -----------------------------------------------------------------------------
> -
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 145.70 PRESS = -6251.52
> Etot = -142853.8179 EKtot = 12999.1687 EPtot = -155852.9865
> BOND = 199.8291 ANGLE = 753.9283 DIHED = 1595.4585
> 1-4 NB = 1194.8248 1-4 EEL = 17423.9459 VDWAALS = 13876.1800
> EELEC = -190897.1533 EHBOND = 0.0000 CONSTRAINT = 0.0000
> EKCMT = 3742.7499 VIRIAL = 76340.5825 VOLUME = 537848.7398
> Density = 0.8249
> Ewald error estimate: 0.1798E-04
> -----------------------------------------------------------------------------
> -
>
>
> COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
> DEVIATION IS TOO LARGE
> NITER, NIT, LL, I AND J ARE : 0 0 590 1144 1146
>
> and my input file is,
>
> Initial md with wat TIP3 model, protein fixed
> &cntrl
> imin=0, ntc=2, ntf=2, tol=0.00001,
> scee=1.2,
> ntx=1, irest=0, cut=10.0,
> ntb=2, ntp=1, npscal=1, pres0=1.0, taup=0.2,
> nstlim=10000, dt=0.02,
> temp0=300.0, tempi=100.0, ig=71277, ntt=1,
> &end
> &wt
> type='TEMP0', istep1=0, istep2=500,
> value1=100.0, value2=300.0,
> &end
> &wt
> type='TEMP0', istep1=500, istep2=10000,
> value1=300.0, value2=300.0,
> &end
> &wt
> type='END',
> &end
> &rst
> iat=0,
> &end
> Hold the protein fixed
> 2000.0
> RES 1 380
> END
> END
>
> Does someone know what is wrong in my input file?
> Thanks in advance.
>
> Difei
>
> Di-Fei Wang, Ph.D
> Department of Chemistry and Biochemistry
> University of Notre Dame
> Notre Dame, IN, 46556
> U.S.A.
> email: dwang_at_nd.edu
> tel:(219)-631-6013(Lab.)
> (219)-251-0836(Home)
> fax:(219)-631-6652
>
>