AMBER Archive (2009)

Subject: [AMBER] temperature rises with igb=1

From: Bala subramanian (bala.biophysics_at_gmail.com)
Date: Tue Mar 17 2009 - 11:35:41 CDT

hello,
I am doing a restrained heating and equilibration of a DNA molecule with
igb=1. I find that the temperature rises heavily during equilibration.
Kindly write me if there is any problem with the input. Here with i am
pasting the input file and corresponding average value for the run.

*3.in*
 &cntrl

imin=0,ntx=1,irest=0,ntpr=100,ntwr=500,ntwx=500,nstlim=20000,dt=0.001,tempi=100.0,temp0=300.0,
tautp=0.5,

ntt=3,gamma_ln=1.0,cut=12,ntc=2,ntf=2,tol=0.000001,ntr=1,restraint_wt=25,restraintmask=':1-22',
  ntb=0,igb=1,intdiel=1,extdiel=80,saltcon=0.1,gbsa=1,rgbmax=15
/

*3.out* A V E R A G E S O V E R 20000 S T E P S

 NSTEP = 20000 TIME(PS) = 20.000 TEMP(K) = 315.72 PRESS =
0.0
 Etot = -3279.9798 EKtot = 594.4523 EPtot =
-3874.4320
 BOND = 173.5187 ANGLE = 338.5309 DIHED =
497.0115
 1-4 NB = 154.3927 1-4 EEL = -2038.4408 VDWAALS =
-418.0539
 EELEC = 644.2022 EGB = -3439.1338 RESTRAINT =
197.1292
 ESURF= 16.4111
 EAMBER (non-restraint) = -4071.5613
 ------------------------------------------------------------------------------
*
4.in*
&cntrl

imin=0,ntx=5,irest=1,ntpr=100,ntwr=500,ntwx=500,nstlim=100000,dt=0.001,tempi=300.0,temp0=300.0,
tautp=0.5,

ntt=3,gamma_ln=1.0,cut=12,ntc=2,ntf=2,tol=0.000001,ntr=1,restraint_wt=25,restraintmask=':1-22',
  ntb=0,igb=1,intdiel=1,extdiel=80,saltcon=0.1,gbsa=1,rgbmax=15
/
*4.out* A V E R A G E S O V E R 100000 S T E P S

 NSTEP = 100000 TIME(PS) = 120.000 TEMP(K) = 336.13 PRESS =
0.0
 Etot = -3132.9746 EKtot = 632.8825 EPtot =
-3765.8571
 BOND = 181.1920 ANGLE = 361.8975 DIHED =
505.7138
 1-4 NB = 158.6175 1-4 EEL = -2047.9551 VDWAALS =
-416.3848
 EELEC = 632.4824 EGB = -3418.2733 RESTRAINT =
260.4555
 ESURF= 16.3972
 EAMBER (non-restraint) = -4026.3126
 ------------------------------------------------------------------------------

*5.in*
 &cntrl

imin=0,ntx=5,irest=1,ntpr=100,ntwr=500,ntwx=500,nstlim=100000,dt=0.001,tempi=300.0,temp0=300.0,
tautp=0.5,

ntt=3,gamma_ln=1.0,cut=12,ntc=2,ntf=2,tol=0.000001,ntr=1,restraint_wt=15,restraintmask=':1-22',
  ntb=0,igb=1,intdiel=1,extdiel=80,saltcon=0.1,gbsa=1,rgbmax=15
/

*5.out*
      A V E R A G E S O V E R 100000 S T E P S

 NSTEP = 100000 TIME(PS) = 220.000 TEMP(K) = 340.17 PRESS =
0.0
 Etot = -3127.9006 EKtot = 640.4851 EPtot =
-3768.3857
 BOND = 184.4660 ANGLE = 375.1764 DIHED =
509.5312
 1-4 NB = 159.1155 1-4 EEL = -2041.3713 VDWAALS =
-412.2985
 EELEC = 568.1845 EGB = -3359.6417 RESTRAINT =
231.9894
 ESURF= 16.4629
 EAMBER (non-restraint) = -4000.3751
 ------------------------------------------------------------------------------

*6.in*
&cntrl

imin=0,ntx=5,irest=1,ntpr=100,ntwr=500,ntwx=500,nstlim=100000,dt=0.001,tempi=300.0,temp0=300.0,
tautp=0.5,

ntt=3,gamma_ln=1.0,cut=12,ntc=2,ntf=2,tol=0.000001,ntr=1,restraint_wt=10,restraintmask=':1-22',
  ntb=0,igb=1,intdiel=1,extdiel=80,saltcon=0.1,gbsa=1,rgbmax=15
/

*6.out* A V E R A G E S O V E R 100000 S T E P S

 NSTEP = 100000 TIME(PS) = 320.000 TEMP(K) =********* PRESS =
0.0
 Etot = NaN EKtot = 3568123.6676 EPtot = NaN
 BOND = 851450.1246 ANGLE = 15111.5468 DIHED =
1984.8352
 1-4 NB = 1179.4403 1-4 EEL = -2064.5821 VDWAALS =
155.2364
 EELEC = 404.5486 EGB = NaN RESTRAINT =
639525195.9927
 ESURF= 28.9927
 EAMBER (non-restraint) = NaN
 ------------------------------------------------------------------------------

*7.in
* &cntrl

imin=0,ntx=5,irest=1,ntpr=100,ntwr=500,ntwx=500,nstlim=250000,dt=0.001,tempi=300.0,temp0=300.0,
tautp=0.5,
  ntt=3,gamma_ln=1.0,cut=12,ntc=2,ntf=2,tol=0.000001,
  ntb=0,igb=1,intdiel=1,extdiel=80,saltcon=0.1,gbsa=1,rgbmax=15
/

*7.out*
 NSTEP = 2600 TIME(PS) = 391.100 TEMP(K) =********* PRESS =
0.0
 Etot = NaN EKtot = 4169332.4319 EPtot = NaN
 BOND = 3755299.6126 ANGLE = 17136.1150 DIHED =
2193.0315
 1-4 NB = 1465.3480 1-4 EEL = -2085.5028 VDWAALS =
200.2644
 EELEC = 449.1234 EGB = NaN RESTRAINT =
0.0000
 ESURF= 30.7391
 ------------------------------------------------------------------------------

I terminated the simulation here.

Thanks,
Bala
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