# Re: [AMBER] Equilibration in multiple steps with decrement in force constants

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Mon, 1 Apr 2019 09:29:41 -0400

Can you send energy info from step 1 of the second equilibration phase?
That might help explain why T goes up.

On Mon, Apr 1, 2019, 7:30 AM Priyabrata Das <pdas.mantu.gmail.com> wrote:

> Here, I am giving both input and output of the first two equilibration
> steps. Please suggest how to proceed.
>
> *Step-1*
> Equilibrate 1000ps MD with restraints force K=20 on DNA at 298K
>
> &cntrl
>
> imin = 0,
>
> irest = 1,
>
> ntx = 7,
>
> ntb = 2,
>
> pres0 = 1.0,
>
> ntp = 1,
>
> taup = 2.0,
>
> cut = 10.0,
>
> ntr = 1,
>
> ntc = 2,
>
> ntf = 2,
>
> tempi = 298.0,
>
> temp0 = 298.0,
>
> ntt = 3,
>
> gamma_ln = 1.0,
>
> nstlim = 500000, dt = 0.002,
>
> ntpr = 100, ntwx = 100, ntwr = 1000, ig=-1
>
> /
>
> Keep DNA fixed with weak restraints
>
> 20.0
>
> RES 1 32
>
> END
>
> END
>
> *Output*
> NSTEP = 100 TIME(PS) = 20.200 TEMP(K) = 298.21 PRESS =
> -932.3
> Etot = -76679.4354 EKtot = 16619.1016 EPtot =
> -93298.5369
> BOND = 265.0071 ANGLE = 916.8113 DIHED =
> 1030.1160
> 1-4 NB = 278.1083 1-4 EEL = -3357.5781 VDWAALS =
> 11809.3495
> EELEC = -104717.0866 EHBOND = 0.0000 RESTRAINT =
> 476.7357
> EAMBER (non-restraint) = -93775.2726
> EKCMT = 7900.7086 VIRIAL = 14255.8939 VOLUME =
> 315704.7851
> Density =
> 0.9001
>
> Step-2
> Equilibriate 1000ps MD with restraints force K=10 on DNA at 298K
>
> &cntrl
>
> imin = 0,
>
> irest = 1,
>
> ntx = 7,
>
> ntb = 2,
>
> pres0 = 1.0,
>
> ntp = 1,
>
> taup = 2.0,
>
> cut = 10.0,
>
> ntr = 1,
>
> ntc = 2,
>
> ntf = 2,
>
> tempi = 298.0,
>
> temp0 = 298.0,
>
> ntt = 3,
>
> gamma_ln = 1.0,
>
> nstlim = 500000, dt = 0.002,
>
> ntpr = 250, ntwx = 250, ntwr = 1000, ig=-1
>
> /
>
> Keep DNA fixed with weak restraints
>
> 10.0
>
> RES 1 32
>
> END
>
> END
>
> Output:
> NSTEP = 250 TIME(PS) = 1020.500 TEMP(K) = 701.97 PRESS =
> 3580.1
> Etot = -35587.7198 EKtot = 39119.7109 EPtot =
> -74707.4307
> BOND = 1944.9083 ANGLE = 3707.3148 DIHED =
> 1732.1500
> 1-4 NB = 502.3380 1-4 EEL = -3517.3746 VDWAALS =
> 12428.6021
> EELEC = -96878.4096 EHBOND = 0.0000 RESTRAINT =
> 5373.0401
> EAMBER (non-restraint) = -80080.4709
> EKCMT = 19143.6718 VIRIAL = -3694.8544 VOLUME =
> 295455.7952
> Density =
> 0.9618
>
>
> On Mon, Apr 1, 2019 at 4:41 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > Yes equilibration is typically done in multiple steps with decreasing
> force
> > constants. However this doesn't use k1 etc. Maybe you can post your input
> > and the section of the output that gives the first energies so we can see
> > what you did and what happened.
> >
> > On Mon, Apr 1, 2019, 6:20 AM Priyabrata Das <pdas.mantu.gmail.com>
> wrote:
> >
> > > Dear all,
> > > I am a beginner in Amber and wanted to know if the equilibration step
> > can
> > > be done in multiple steps with decreasing the force constant.
> > >
> > > I am working on DNA molecular dynamics simulation. Prior to
> > equilibration,
> > > I have done minimization and heating(from 0 to 300k with K=20 for
> 20ps).
> > > When equilibrating the system with decreasing force constant (K1=20,
> > K2=10,
> > > K3=5, K4=1, and without constraints). During the starting of the second
> > > step of equilibration (K2=10) temperature is shooting up to 700 K.
> After
> > > that everything is going well. Should I continue or this can cause any
> > > problem?
> > >
> > > Thanks
> > > Priyabrata Das
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Received on Mon Apr 01 2019 - 07:00:02 PDT
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