Re: [AMBER] temperature rises with igb=1

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Tue, 17 Mar 2009 16:44:32 +0000

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
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