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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> >
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Received on Mon Apr 01 2019 - 05:00:03 PDT
