AMBER Archive (2003)

Subject: Re: MD went crazy

From: Youyi Peng (pengyo_at_UMDNJ.EDU)
Date: Fri Apr 18 2003 - 13:33:26 CDT

Drs. Simmerling and Crowley:
  Thank you for your advice.
I tried the MD without restraints and with different force constant. It looks
that distance restraint is fine but backbone restaint causes the problem. Even
with the force constant 0.5 kcal/mol-A^2, the temp. will increse to 340K from
300K. So if I want to fix the backbone during MD, what can I do?
 Thanks a lot!

Carlos Simmerling wrote:

> if the step 1 restraint energies are this high,
> then the initial coordinates do not satify the restraints.
> check them to see what is wrong.
> carlos
>
> ----- 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 1:36 PM
> Subject: Re: MD went crazy
>
> > 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
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > >
> > > >
> >
> >