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 - 10:30:03 PDT
