AMBER Archive (2003)

Subject: Re: MD went crazy

From: Youyi Peng (pengyo_at_UMDNJ.EDU)
Date: Fri Apr 18 2003 - 11:17:24 CDT

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
> >
> >
> >
> >
> >
> >
> >