AMBER Archive (2003)

Subject: Re: MD went crazy

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Apr 18 2003 - 11:17:11 CDT

this still says NTEP=100. that is NOT step 1.
please send output for step 1. if you don't have it,
rerun for 100 steps with ntpr=1.

----- Original Message -----
From: "Youyi Peng" <pengyo_at_UMDNJ.EDU>
To: "Carlos Simmerling" <carlos.simmerling_at_stonybrook.edu>;
<amber_at_heimdal.compchem.ucsf.edu>
Sent: Friday, April 18, 2003 12:17 PM
Subject: Re: MD went crazy

> At step one, the energy is already high. Below are energy summaries for
step
> 1 and step 2.
>
> NSTEP = 100 TIME(PS) = 10.100 TEMP(K) =********* PRESS = 0.0
> Etot = ************ EKtot = ************ EPtot = 2030503.4104
> BOND = 680589.0727 ANGLE = 195442.5670 DIHED = 15070.5764
> 1-4 NB = 147731.1861 1-4 EEL = 515.4914 VDWAALS = 119163.7687
> EELEC = -1082.3027 EHBOND = 0.0000 RESTRAINT = 873073.0509
> EAMBER (non-restraint) = 1157430.3595
> -------------------------------------------------------------------------
-----
>
>
============================================================================
===
>
> NMR restraints for step 100
> Energy (this step): Bond = 68.602 Angle = 0.000 Torsion =
> 0.000
> Energy (tot. run) : Bond = 29.972 Angle = 0.000 Torsion =
> 0.000
>
> DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
> This step Entire run This step Entire
run
> ave. rms ave. rms ave. rms ave.
rms
> Bond 4.130 4.130 2.103 2.103 3.680 3.680 1.699
> 1.699
> Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000
> 0.000
> Torsion 0.000 0.000 0.000 0.000 0.000 0.000 0.000
> 0.000
>
> NSTEP = 200 TIME(PS) = 10.200 TEMP(K) =********* PRESS = 0.0
> Etot = ************ EKtot = ************ EPtot = 2515784.3097
> BOND = 785400.7401 ANGLE = 208233.2922 DIHED = 15222.1171
> 1-4 NB = 447817.5405 1-4 EEL = 578.4161 VDWAALS = 113434.8320
> EELEC = -1240.8367 EHBOND = 0.0000 RESTRAINT = 946338.2084
> EAMBER (non-restraint) = 1569446.1013
> -------------------------------------------------------------------------
-----
>
>
============================================================================
===
>
> NMR restraints for step 200
> Energy (this step): Bond = 11.717 Angle = 0.000 Torsion =
> 0.000
> Energy (tot. run) : Bond = 28.517 Angle = 0.000 Torsion =
> 0.000
>
> DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
> This step Entire run This step Entire
run
> ave. rms ave. rms ave. rms ave.
rms
> Bond 1.286 1.286 2.078 2.078 0.836 0.836 1.651
> 1.651
> Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000
> 0.000
> Torsion 0.000 0.000 0.000 0.000 0.000 0.000 0.000
> 0.000
>
> Carlos Simmerling wrote:
>
> > please provide output that lists the energies
> > at the first step- by the time we see what is going
> > on, it already has the vlimit warnings. it is important
> > to see the first step restraint energies, and how quickly
> > the energies rise, etc.
> > ===================================================================
> > Carlos L. Simmerling, Ph.D.
> > Assistant Professor Phone: (631) 632-1336
> > Center for Structural Biology Fax: (631) 632-1555
> > Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
> > Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
> > ===================================================================
> >
> > ----- Original Message -----
> > From: "Youyi Peng" <pengyo_at_UMDNJ.EDU>
> > To: <amber_at_heimdal.compchem.ucsf.edu>
> > Sent: Friday, April 18, 2003 11:20 AM
> > Subject: MD went crazy
> >
> > > Hi,
> > > I initiated MD by heating the ligand-protein complex with no
> > > constraints on the atoms from 0 to 300K in 10 ps.Then 100ps
eqilibration
> > > at the constant temp. 300K was performed on restrained backbone and
> > > distance. I got crazy MD output. THe energy and temp. went to very
high
> > > and a lot of vlimit warnings. Below is the input file and part of the
> > > output file. Please take a look for me.
> > > Thank you very much and happy good Friday!
> > >
> > > MDIN:
> > > dynamics w/o belly on protein, 9.0 cut, with constraints of backbone
and
> > > distance
> > > &cntrl
> > > nmropt = 1,
> > > ntx = 5, irest = 1, ntrx = 1, ntxo = 1,
> > > ntpr = 100, ntwx = 1000, ntwv = 0, ntwe = 0,
> > >
> > > ntf = 1, ntb = 0,
> > > cut = 9.0, nsnb = 10, dielc=4.0
> > >
> > > ibelly = 0, ntr = 1,
> > >
> > > imin = 0,
> > > nstlim = 100000,
> > > nscm = 0, dt = 0.001,
> > >
> > > temp0 = 300.0, tempi = 300.0,
> > > heat = 0.0,
> > > ntt = 1,
> > > tautp = 2.0,
> > > vlimit = 20.0,
> > >
> > >
> > > ntc = 1, tol = 0.00001,
> > > &end
> > >
> > > &ewald
> > > eedmeth=5,
> > > &end
> > >
> > > &wt
> > > type='END' ,
> > > &end
> > >
> > > LISTOUT=POUT
> > > DISANG=RST.dist
> > >
> > > Hold the backbone restrainted
> > > 500.0
> > > FIND
> > > * CT * *
> > > * N * *
> > > * C * *
> > > * O * *
> > > SEARCH
> > > RES 1 293
> > > END
> > > END
> > >
> > > OUTPUT
> > > vlimit exceeded for step 992; vmax = 1297679.08
> > > vlimit exceeded for step 993; vmax = 200557512.
> > > vlimit exceeded for step 994; vmax = 86296.6221
> > > vlimit exceeded for step 995; vmax = 530655.444
> > > vlimit exceeded for step 996; vmax = 719129.926
> > > vlimit exceeded for step 997; vmax = 2.54845046E+09
> > > vlimit exceeded for step 998; vmax = 97404.1622
> > > vlimit exceeded for step 999; vmax = 330667.274
> > >
> > > NSTEP = 1000 TIME(PS) = 11.000 TEMP(K) =********* PRESS =
0.0
> > >
> > > Etot = ************ EKtot = ************ EPtot =
> > > 3906732.9101
> > > BOND = 865895.1848 ANGLE = 223527.1116 DIHED =
> > > 15612.3010
> > > 1-4 NB = 1509819.0853 1-4 EEL = 546.5250 VDWAALS =
> > > 163607.4823
> > > EELEC = -1106.9859 EHBOND = 0.0000 RESTRAINT =
> > > 1128832.2060
> > > EAMBER (non-restraint) = 2777900.7040
> > >
> > >
> > >
> > >
> > >
> > >
> > >
>
>