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From: Priyabrata Das <pdas.mantu.gmail.com>

Date: Mon, 1 Apr 2019 22:34:08 +0530

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
*

*> > > > _______________________________________________
*

*> > > > AMBER mailing list
*

*> > > > AMBER.ambermd.org
*

*> > > > http://lists.ambermd.org/mailman/listinfo/amber
*

*> > > >
*

*> > > _______________________________________________
*

*> > > AMBER mailing list
*

*> > > AMBER.ambermd.org
*

*> > > http://lists.ambermd.org/mailman/listinfo/amber
*

*> > >
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > AMBER.ambermd.org
*

*> > http://lists.ambermd.org/mailman/listinfo/amber
*

*> >
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

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Received on Mon Apr 01 2019 - 10:30:03 PDT

Date: Mon, 1 Apr 2019 22:34:08 +0530

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:

_______________________________________________

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Received on Mon Apr 01 2019 - 10:30:03 PDT

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