AMBER Archive (2003)

Subject: Re: MD went crazy

From: Michael Crowley (crowley_at_scripps.edu)
Date: Fri Apr 18 2003 - 12:30:53 CDT

Dear Youyi,
As I suspected, the problem is in your restraints.
They are pulling the system apart in an unnatural way.
Try running without the restraints and then figure out
which restraints are not correct.
Good luck,
Mike

-----------------------------------------------------------------
Physical mail: Dr. Michael F. Crowley
                 Department of Molecular Biology, TPC6
                 The Scripps Research Institute
                 10550 North Torrey Pines Road
                 La Jolla, California 92037

Electronic mail: crowley_at_scripps.edu
Telephone: 858/784-9290
Fax: 858/784-8688
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On Fri, 18 Apr 2003, Youyi Peng wrote:

> This is the summary for step 1. TEMP is extremely high: 6238.65K. This MD run
> followed the previous run without restraints (the last step is shown below).
>
> STEP1 for this run:
> Local SIZE OF NONBOND LIST = 795677
> | TOTAL SIZE OF NONBOND LIST = 795677
> vlimit exceeded for step 0; vmax = 24.0628678
>
> NSTEP = 1 TIME(PS) = 10.001 TEMP(K) = 6238.65 PRESS = 0.0
> Etot = ************ EKtot = 88628.9015 EPtot = ************
> BOND = 1485.1811 ANGLE = 2344.0215 DIHED = 2626.9553
> 1-4 NB = 1229.1304 1-4 EEL = 826.5103 VDWAALS = -2170.8074
> EELEC = -1453.0778 EHBOND = 0.0000 RESTRAINT = ************
> EAMBER (non-restraint) = 4887.9134
> ------------------------------------------------------------------------------
>
> ===============================================================================
>
> NMR restraints for step 1
> Energy (this step): Bond = 25.128 Angle = 0.000 Torsion = 0.000
> Energy (tot. run) : Bond = 25.128 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 1.956 1.956 1.956 1.956 1.506 1.506 1.506 1.506
> 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
> ===============================================================================
>
> The last step for previous run:
>
> NSTEP = 10000 TIME(PS) = 10.000 TEMP(K) = 297.41 PRESS = 0.0
> Etot = 9143.5794 EKtot = 4225.1734 EPtot = 4918.4060
> BOND = 1497.6732 ANGLE = 2357.3947 DIHED = 2630.4760
> 1-4 NB = 1230.9899 1-4 EEL = 825.9995 VDWAALS = -2168.5049
> EELEC = -1455.6224 EHBOND = 0.0000 RESTRAINT = 0.0000
> ------------------------------------------------------------------------------
>
>
>
> Carlos Simmerling wrote:
>
> > 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
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > >
> > >
>
>
>