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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Received on Wed Mar 18 2009 - 01:17:29 PDT
