AMBER Archive (2003)

Subject: AMBER: Dynamics and Simulated Annealing

From: Narang Manpreet Kaur (preetdbs_at_iitr.ernet.in)
Date: Fri Jul 25 2003 - 08:03:52 CDT

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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