AMBER Archive (2003)

Subject: Re: MD went crazy

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Apr 18 2003 - 14:04:49 CDT

at step 1 your restraint energy is still 10,000 kcal/mol.
you need to figure out why your restraints do not
match your input coordinates. at step 1, you should
have nearly zero restraint energy (listed incorrectly by
amber as CONstraint). When that happens, then you can
do a production MD run and see what happens.
Carlos
===================================================================
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: "Carlos Simmerling" <carlos.simmerling_at_stonybrook.edu>;
<amber_at_heimdal.compchem.ucsf.edu>
Sent: Friday, April 18, 2003 2:55 PM
Subject: Re: MD went crazy

> I guess you want the output for force constant 0.5. Here they are.
>
> NSTEP = 1 TIME(PS) = 10.001 TEMP(K) = 299.62 PRESS = 0.0
> Etot = 19509.8677 EKtot = 4256.5489 EPtot = 15253.3188
> 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 = 10365.4054
> EAMBER (non-restraint) = 4887.9134
> -------------------------------------------------------------------------
-----
>
>
>
> NSTEP = 2 TIME(PS) = 10.002 TEMP(K) = 300.97 PRESS = 0.0
> Etot = 19512.1920 EKtot = 4275.6783 EPtot = 15236.5136
> BOND = 1480.1913 ANGLE = 2333.3413 DIHED = 2623.9937
> 1-4 NB = 1227.3937 1-4 EEL = 826.9741 VDWAALS = -2170.9020
> EELEC = -1450.8055 EHBOND = 0.0000 RESTRAINT = 10366.3270
> EAMBER (non-restraint) = 4870.1866
> -------------------------------------------------------------------------
-----
>
>
>
> NSTEP = 3 TIME(PS) = 10.003 TEMP(K) = 300.88 PRESS = 0.0
> Etot = 19509.7266 EKtot = 4274.3763 EPtot = 15235.3503
> BOND = 1490.2147 ANGLE = 2327.4749 DIHED = 2621.9514
> 1-4 NB = 1225.9541 1-4 EEL = 827.4478 VDWAALS = -2169.1865
> EELEC = -1454.9689 EHBOND = 0.0000 RESTRAINT = 10366.4630
> EAMBER (non-restraint) = 4868.8873
> -------------------------------------------------------------------------
-----
>
>
>
> NSTEP = 4 TIME(PS) = 10.004 TEMP(K) = 300.19 PRESS = 0.0
> Etot = 19513.8948 EKtot = 4264.6915 EPtot = 15249.2034
> BOND = 1501.0549 ANGLE = 2328.1776 DIHED = 2621.0000
> 1-4 NB = 1224.9311 1-4 EEL = 827.9668 VDWAALS = -2166.8872
> EELEC = -1452.8313 EHBOND = 0.0000 RESTRAINT = 10365.7914
> EAMBER (non-restraint) = 4883.4120
> -------------------------------------------------------------------------
-----
>
>
>
> NSTEP = 5 TIME(PS) = 10.005 TEMP(K) = 300.05 PRESS = 0.0
> Etot = 19509.0390 EKtot = 4262.6168 EPtot = 15246.4223
> BOND = 1495.8537 ANGLE = 2335.7618 DIHED = 2621.1293
> 1-4 NB = 1224.3465 1-4 EEL = 828.5270 VDWAALS = -2165.0672
> EELEC = -1458.4626 EHBOND = 0.0000 RESTRAINT = 10364.3339
> EAMBER (non-restraint) = 4882.0884
> -------------------------------------------------------------------------
-----
>
> .
> .
> .
> .
> .
> NSTEP = 32 TIME(PS) = 10.032 TEMP(K) = 315.90 PRESS = 0.0
> Etot = 19498.8441 EKtot = 4487.8493 EPtot = 15010.9948
> BOND = 1452.3568 ANGLE = 2381.3638 DIHED = 2622.1332
> 1-4 NB = 1250.9774 1-4 EEL = 828.9638 VDWAALS = -2176.2030
> EELEC = -1469.4974 EHBOND = 0.0000 RESTRAINT = 10120.9001
> EAMBER (non-restraint) = 4890.0947
> -------------------------------------------------------------------------
-----
>
>
>
> NSTEP = 33 TIME(PS) = 10.033 TEMP(K) = 318.23 PRESS = 0.0
> Etot = 19495.8606 EKtot = 4520.8692 EPtot = 14974.9914
> BOND = 1441.3492 ANGLE = 2377.9541 DIHED = 2620.1685
> 1-4 NB = 1250.9751 1-4 EEL = 828.7977 VDWAALS = -2177.7700
> EELEC = -1471.3100 EHBOND = 0.0000 RESTRAINT = 10104.8268
> EAMBER (non-restraint) = 4870.1647
> -------------------------------------------------------------------------
-----
>
>
>
> NSTEP = 34 TIME(PS) = 10.034 TEMP(K) = 319.80 PRESS = 0.0
> Etot = 19499.4071 EKtot = 4543.2099 EPtot = 14956.1972
> BOND = 1442.9031 ANGLE = 2371.8018 DIHED = 2619.4572
> 1-4 NB = 1251.0418 1-4 EEL = 828.6447 VDWAALS = -2178.2709
> EELEC = -1467.6949 EHBOND = 0.0000 RESTRAINT = 10088.3147
> EAMBER (non-restraint) = 4867.8826
> -------------------------------------------------------------------------
-----
>
>
>
> NSTEP = 35 TIME(PS) = 10.035 TEMP(K) = 320.93 PRESS = 0.0
> Etot = 19500.3084 EKtot = 4559.2268 EPtot = 14941.0816
> BOND = 1450.2755 ANGLE = 2364.2386 DIHED = 2620.1680
> 1-4 NB = 1251.2244 1-4 EEL = 828.5121 VDWAALS = -2177.3447
> EELEC = -1467.3313 EHBOND = 0.0000 RESTRAINT = 10071.3392
> EAMBER (non-restraint) = 4869.7424
> -------------------------------------------------------------------------
-----
>
>
>
> Carlos Simmerling wrote:
>
> > send the first few steps of output again.
> > ----- 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 2:33 PM
> > Subject: Re: MD went crazy
> >
> > > 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
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > >
> > > > > > >
> > > > >
> > > > >
> > >
> > >
>
>