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

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Mon, 1 Apr 2019 14:38:16 -0400

This is truncated in my screen, please send the entire energy/time section
of the output at step 1.

On Mon, Apr 1, 2019, 1:04 PM Priyabrata Das <pdas.mantu.gmail.com> wrote:

> Energies of the second equilibration phase are :
> Etot = -35587.7198 EKtot = 39119.7109 EPtot =
> -74707.4307,
>
>
>
>
> On Mon, Apr 1, 2019 at 7:01 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > 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 - 12:00:03 PDT
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