Re: AMBER: Dynamics and Simulated Annealing

From: Carlos Simmerling <carlos.simmerling.sunysb.edu>
Date: Fri, 25 Jul 2003 12:53:38 -0400

in order to use the weight change (for the temperature)
you need to set nmropt=1 even if you have no restraints.
you will need to specify a dummy restraint using
&rst iat(1)=0, &end .
make sure to check the sander output file, it will tell
you if it correctly read the temperature change. don't
let the simulation continue until it lets you know
that your input was correct.
Carlos

----- Original Message -----
From: "Narang Manpreet Kaur" <preetdbs.iitr.ernet.in>
To: <amber.scripps.edu>
Sent: Friday, July 25, 2003 9:03 AM
Subject: AMBER: Dynamics and Simulated Annealing


> Dear AMBER users,
> I have done minimization on the drug molecule
> folllwed by molecular dynamics at constant temperature of 300K. Now I want
> to perform the molecular dynamics by raising the temperature from 300
> to 500K and then cool the system back to 300K. I have not given any
> NMR restraints for the system i.e.nmropt=0.
>
> --------------------------------------------------------------------------
---------------------------------------------------------------------
> Here is my input file:
> &cntrl
> imin=0, cut=9.0, nstlim=4500, temp0= 300, tempi=500,
> ntb=1, scee=1.2, ntx=7, irest=1, ntwe=100, ntwx=100, ntwe=100 ntpr=100,
> vlimit=20
> &end
> &wt type='TEMP0', istep1=0,istep2=1500,value1=300.0,
> value2=500.0, &end
> &wt type='TEMP0', istep1=1500,istep2=4500,value1=500.0,
> value2=500.0, &end
> &wt type='END' &end
>
> &wt type='TAUTP', istep1=0,istep2=1500,value1=0.2,
> value2=0.2, &end
> &wt type='TAUTP', istep1=1500,istep2=4500,value1=4.0,
> value2=2.0, &end
> &wt type='END' &end
> --------------------------------------------------------------------------
-------
> Here is my output for the first few psecs: NSTEP = 1 TIME(PS) = 15.001
> TEMP(K) = 278.41 PRESS = 0.00
> Etot = -6001.4549 EKtot = 2078.0500 EPtot = -8079.5048
> BOND = 1458.7062 ANGLE = 17.6848 DIHED = 27.9723
> 1-4 NB = 23.2711 1-4 EEL = -13.1509 VDWAALS = 1702.5947
> EELEC = -11296.5830 EHBOND = 0.0000 CONSTRAINT = 0.0000
> Ewald error estimate: 0.1301E-03
> --------------------------------------------------------------------------
------
> NSTEP = 100 TIME(PS) = 15.100 TEMP(K) = 275.38 PRESS = 0.00
> Etot = -5999.9069 EKtot = 2055.4018 EPtot = -8055.3086
> BOND = 1481.5058 ANGLE = 18.8310 DIHED = 26.8629
> 1-4 NB = 23.5210 1-4 EEL = -13.5710 VDWAALS = 1745.3611
> EELEC = -11337.8195 EHBOND = 0.0000 CONSTRAINT = 0.0000
> Ewald error estimate: 0.1093E-03
> --------------------------------------------------------------------------
-------
> NSTEP = 200 TIME(PS) = 15.200 TEMP(K) = 275.02 PRESS = 0.00
> Etot = -6001.8174 EKtot = 2052.7493 EPtot = -8054.5667
> BOND = 1343.5375 ANGLE = 20.1631 DIHED = 24.2781
> 1-4 NB = 22.1164 1-4 EEL = -12.3693 VDWAALS = 1671.2993
> EELEC = -11123.5918 EHBOND = 0.0000 CONSTRAINT = 0.0000
> Ewald error estimate: 0.2948E-03
> --------------------------------------------------------------------------
------
> NSTEP = 300 TIME(PS) = 15.300 TEMP(K) = 277.55 PRESS = 0.00
> Etot = -6005.2315 EKtot = 2071.5758 EPtot = -8076.8073
> BOND = 1448.1803 ANGLE = 18.3997 DIHED = 27.2054
> 1-4 NB = 20.6311 1-4 EEL = -12.9090 VDWAALS = 1723.1856
> EELEC = -11301.5004 EHBOND = 0.0000 CONSTRAINT = 0.0000
> Ewald error estimate: 0.1985E-03
> --------------------------------------------------------------------------
-------
> NSTEP = 400 TIME(PS) = 15.400 TEMP(K) = 280.08 PRESS = 0.00
> Etot = -6007.9118 EKtot = 2090.4776 EPtot = -8098.3893
> BOND = 1322.5543 ANGLE = 23.6840 DIHED = 23.8060
> 1-4 NB = 22.1670 1-4 EEL = -13.3922 VDWAALS = 1665.4033
> EELEC = -11142.6117 EHBOND = 0.0000 CONSTRAINT = 0.0000
> Ewald error estimate: 0.2109E-03
> --------------------------------------------------------------------------

----
> and for the last few steps.......
> NSTEP = 4100 TIME(PS) = 19.100 TEMP(K)= 276.02 PRESS = 0.00
>  Etot = -6004.7688 EKtot = 2060.1471 EPtot = -8064.9159
>  BOND = 1393.1937 ANGLE = 23.5853 DIHED = 16.4406
>  1-4 NB = 22.3661 1-4 EEL = -13.2189 VDWAALS = 1718.4916
>  EELEC = -11225.7742 EHBOND = 0.0000 CONSTRAINT = 0.0000
>  Ewald error estimate:  0.1108E-03
>
>
> --------------------------------------------------------------------------
----
>  NSTEP = 4200 TIME(PS) = 19.200 TEMP(K) = 273.75 PRESS = 0.00
>  Etot = -6001.1754 EKtot = 2043.2050 EPtot = -8044.3803
>  BOND = 1302.3835 ANGLE = 23.2105 DIHED = 20.2206
>  1-4 NB = 22.4704 1-4 EEL = -13.6531 VDWAALS = 1643.2283
>  EELEC = -11042.2406 EHBOND = 0.0000 CONSTRAINT = 0.0000
>  Ewald error estimate:  0.3797E-03
> --------------------------------------------------------------------------
----
>  NSTEP = 4300 TIME(PS) = 19.300 TEMP(K) = 271.00 PRESS = 0.00
>  Etot = -6006.2303 EKtot = 2022.7130 EPtot = -8028.9432
>  BOND = 1228.8724 ANGLE = 24.6143 DIHED = 25.8352
>  1-4 NB = 22.3572 1-4 EEL = -13.9670 VDWAALS = 1578.1559
>  EELEC = -10894.8113 EHBOND = 0.0000 CONSTRAINT = 0.0000
>  Ewald error estimate:  0.4115E-04
> --------------------------------------------------------------------------
----
>  NSTEP = 4400 TIME(PS) = 19.400 TEMP(K) = 271.37 PRESS = 0.00
>  Etot = -6001.7217 EKtot = 2025.4627 EPtot = -8027.1844
>  BOND = 1427.3722 ANGLE = 21.7686 DIHED = 24.1716
>  1-4 NB = 22.6056 1-4 EEL = -14.2983 VDWAALS = 1539.8873
>  EELEC = -11048.6915 EHBOND = 0.0000 CONSTRAINT = 0.0000
> --------------------------------------------------------------------------
-----
> NSTEP = 4500 TIME(PS) = 19.500 TEMP(K) = 268.06 PRESS = 0.00
>  Etot = -6004.6063 EKtot = 2000.7459 EPtot = -8005.3523
>  BOND = 1255.6839 ANGLE = 22.6208 DIHED = 24.2798
>  1-4 NB = 22.3409 1-4 EEL = -13.4647 VDWAALS = 1616.2280
>  EELEC = -10933.0410 EHBOND = 0.0000 CONSTRAINT = 0.0000
>  Ewald error estimate:  0.1651E-03
> --------------------------------------------------------------------------
----
>       A V E R A G E S O V E R 4500 S T E P S
>
>  NSTEP = 4500 TIME(PS) = 19.500 TEMP(K) = 274.92 PRESS = 0.00
>  Etot = -6003.5603 EKtot = 2051.9459 EPtot = -8055.5062
>  BOND = 1368.3559 ANGLE = 20.7848 DIHED = 23.5796
>  1-4 NB = 22.7093 1-4 EEL = -13.3151 VDWAALS = 1682.0123
>  EELEC = -11159.6329 EHBOND = 0.0000 CONSTRAINT = 0.0000
>  Ewald error estimate:  0.1553E-03
> --------------------------------------------------------------------------
----
>  R M S F L U C T U A T I O N S
>  NSTEP = 4500 TIME(PS) = 19.500 TEMP(K) = 3.79 PRESS = 0.00
>  Etot = 2.7745 EKtot = 28.3126 EPtot = 29.3989
>  BOND = 58.7868 ANGLE = 2.2078 DIHED = 3.7760
>  1-4 NB = 1.2909 1-4 EEL = 0.4203 VDWAALS = 50.6529
>  EELEC = 101.1463 EHBOND = 0.0000 CONSTRAINT = 0.0000
>  Ewald error estimate:  0.1275E-03
> --------------------------------------------------------------------------
----
> | | ELAPSED TIME = 2054.412 TOTAL TIME = 2054.412 |
>    Nonbond Ewald pairlist time components:
> | map, save_t = 1.63 0.08
> |grid setup_t = 0.00 0.00
> | grid ucell_t = 0.17 0.01
> | grid image_t = 0.22 0.01
> | build list_t = 159.63 7.77
> | total list_t = 161.64 7.87
>    Nonbond Ewald force time components:
> | zero ene,force = 0.36 0.02
> | map = 0.00 0.00
> | map,adjust = 17.58 0.86
> | self energy = 0.07 0.00
> | 1-dimb-spline= 23.01 1.12
> | grid charges = 129.87 6.32
> | scalar sum = 130.28 6.34
> | grad sum = 184.31 8.97
> | FFT = 139.16 6.77
> | Recip force = 606.6329.53
> | Direct force = 1221.74 59.47
> | adjust masked = 9.34 0.45
> | accum force = 0.07 0.00
> | finish virial = 4.03 0.20
> | mfct4 = 0.05 0.00
> |f_wait = 0.13 0.01
> | stack_time = 0.23 0.01
> | total force = 1860.22 90.55
>   Routine Sec % |
> ----------------------------
> | Nonbond 2029.89 98.81
> |Bond 3.34 0.16
> | Angle 1.35 0.07
> | Dihedral 5.19 0.25
> | Shake 0.00 0.00
> |GBrad 0.00 0.00
> | Force 0.00 0.00
> | Other 14.64 0.71
> |
> ----------------------------
> | Total 2054.41 0.57 Hours
> | Nonsetup 2054.04 99.98%
> | Highest rstack allocated:  122914
> | MAX_RSTACK= 1600000
> |Highest istack allocated:  2504
> | MAX_ISTACK = 100000
> | Setup wallclock  0 seconds
> | Nonsetup wallclock 2091 seconds
> --------------------------------------------------------------------------
-----
> The tempearature has not reached the desired 500K and back to 300 in
> fact it was between 275-280 in the entire run. I want to know how this can
> be achived in vaccuum and in  water. The file input given is for the
> molecule in water.
> Any help in this regard will be appreciated
>
>
> Manpreet Kaur NDarang
> Research Scholar
> Deptt. Biotechnology
> Indian Institute of Technology Roorkee (IITR)
> Roorkee, 247 667
>
>
>
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Received on Fri Jul 25 2003 - 17:53:00 PDT