your restraints are very strong, perhaps causing problems with time integration.
it's hard to analyze since we don't know what your reference structure
is during these steps, or your initial structure source, or your
equilibration procedure before these steps.
I would suggest using a longer cutoff and not setting rgbmax, and
perhaps weaker restraints and see if the problem goes away.
On Tue, Mar 17, 2009 at 12:35 PM, Bala subramanian
<bala.biophysics.gmail.com> wrote:
> 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 - 01:17:25 PDT
