Dr. Simmerling
Thanks for the reply
Explicit heating for 2ns although it heats up for the 1st ns only, then equilib
&cntrl
imin=0, irest=0, ntx=1,
ntpr=1000, ntwx=1000, nstlim=1000000,
dt=0.002, ntt=3, tempi=100.0,
temp0=300.0, tautp=2.0, ig=-1,
ntp=0, ntc=2, ntf=2, cut=10,
ntb=1, nmropt=1, nsnb=20, ibelly=0,
gamma_ln=5.0, ntwr=1000, ioutfm=1,
nmropt=1, ntr=1, igb=0,
restraintmask="!:WAT", restraint_wt=100.0,
&end
&wt type='DUMPFREQ', istep1=10 /
&wt type='END' /
DISANG=dist_nmropt.RST
DUMPAVE=dist_vs_nmroptchange_heat
LISTIN=POUT
LISTOUT=POUT
/
&wt
TYPE='TEMP0', ISTEP1=1, ISTEP2=100000,
VALUE1=100.0, VALUE2=150.0,
&wt type='TEMP0', istep1=100001,istep2=200000,value1=150.0,
value2=200.0, /
&wt type='TEMP0', istep1=200001, istep2=300000, value1=200.0,
value2=250.0, /
&wt type='TEMP0', istep1=300001, istep2=500000, value1=250.0,
value2=300.0, /
&wt TYPE='END' /
Here is a few initial and final steps of output file:
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 149.22 PRESS = 0.0
Etot = -448881.6850 EKtot = 30629.8965 EPtot = -479511.5815
BOND = 34.9333 ANGLE = 126.3831 DIHED = 464.9043
1-4 NB = 174.1324 1-4 EEL = -2489.3083 VDWAALS = 99902.5797
EELEC = -577725.2058 EHBOND = 0.0000 RESTRAINT = 0.0000
EAMBER (non-restraint) = -479511.5815
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 299.85 PRESS = 0.0
Etot = -264426.4753 EKtot = 61551.2461 EPtot = -325977.7214
BOND = 167.5261 ANGLE = 294.5189 DIHED = 501.8281
1-4 NB = 179.0188 1-4 EEL = -2487.8423 VDWAALS = 48271.7345
EELEC = -373234.0310 EHBOND = 0.0000 RESTRAINT = 329.5254
EAMBER (non-restraint) = -326307.2468
------------------------------------------------------------------------------
NMR restraints: Bond = 0.003 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 2000 TIME(PS) = 4.000 TEMP(K) = 300.27 PRESS = 0.0
Etot = -263166.8095 EKtot = 61635.7578 EPtot = -324802.5674
BOND = 166.8201 ANGLE = 266.8136 DIHED = 495.5450
1-4 NB = 177.8956 1-4 EEL = -2504.5175 VDWAALS = 47073.3985
EELEC = -370769.9505 EHBOND = 0.0000 RESTRAINT = 291.4279
EAMBER (non-restraint) = -325093.9952
------------------------------------------------------------------------------
NMR restraints: Bond = 0.149 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 3000 TIME(PS) = 6.000 TEMP(K) = 298.68 PRESS = 0.0
Etot = -263014.6600 EKtot = 61310.9844 EPtot = -324325.6444
BOND = 176.0163 ANGLE = 269.2227 DIHED = 501.4915
1-4 NB = 177.5970 1-4 EEL = -2479.1518 VDWAALS = 47036.0648
EELEC = -370339.8436 EHBOND = 0.0000 RESTRAINT = 332.9588
EAMBER (non-restraint) = -324658.6031
------------------------------------------------------------------------------
NMR restraints: Bond = 0.241 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 4000 TIME(PS) = 8.000 TEMP(K) = 300.70 PRESS = 0.0
Etot = -263429.3307 EKtot = 61724.9609 EPtot = -325154.2917
BOND = 153.1855 ANGLE = 280.3702 DIHED = 492.0673
1-4 NB = 180.0525 1-4 EEL = -2485.8391 VDWAALS = 47188.3332
EELEC = -371294.4587 EHBOND = 0.0000 RESTRAINT = 331.9974
EAMBER (non-restraint) = -325486.2891
------------------------------------------------------------------------------
NMR restraints: Bond = 0.078 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 300.40 PRESS = 0.0
Etot = -263026.5041 EKtot = 61664.1406 EPtot = -324690.6447
BOND = 156.8553 ANGLE = 280.1285 DIHED = 502.6877
1-4 NB = 184.7591 1-4 EEL = -2497.8783 VDWAALS = 46090.6148
EELEC = -369761.2406 EHBOND = 0.0000 RESTRAINT = 353.4288
EAMBER (non-restraint) = -325044.0735
------------------------------------------------------------------------------
NMR restraints: Bond = 0.031 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 6000 TIME(PS) = 12.000 TEMP(K) = 300.61 PRESS = 0.0
Etot = -262326.0077 EKtot = 61705.8672 EPtot = -324031.8748
BOND = 169.3867 ANGLE = 288.1203 DIHED = 496.4722
1-4 NB = 183.6998 1-4 EEL = -2484.6215 VDWAALS = 46028.6278
EELEC = -369039.0011 EHBOND = 0.0000 RESTRAINT = 325.4411
EAMBER (non-restraint) = -324357.3160
------------------------------------------------------------------------------
.
.
.
.
.
.
.
.
.
NSTEP = 992000 TIME(PS) = 1984.000 TEMP(K) = 300.06 PRESS = 0.0
Etot = -267655.5825 EKtot = 61593.0078 EPtot = -329248.5903
BOND = 155.0921 ANGLE = 272.7599 DIHED = 498.1022
1-4 NB = 176.4854 1-4 EEL = -2473.5722 VDWAALS = 47438.5981
EELEC = -375652.0817 EHBOND = 0.0000 RESTRAINT = 336.0259
EAMBER (non-restraint) = -329584.6162
------------------------------------------------------------------------------
NMR restraints: Bond = 0.083 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 993000 TIME(PS) = 1986.000 TEMP(K) = 299.47 PRESS = 0.0
Etot = -267649.6389 EKtot = 61471.4922 EPtot = -329121.1311
BOND = 163.6158 ANGLE = 277.3867 DIHED = 495.8588
1-4 NB = 179.4712 1-4 EEL = -2496.8573 VDWAALS = 47637.2498
EELEC = -375715.5974 EHBOND = 0.0000 RESTRAINT = 337.7411
EAMBER (non-restraint) = -329458.8722
------------------------------------------------------------------------------
NMR restraints: Bond = 0.800 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 994000 TIME(PS) = 1988.000 TEMP(K) = 299.67 PRESS = 0.0
Etot = -267493.3604 EKtot = 61514.4609 EPtot = -329007.8213
BOND = 153.2131 ANGLE = 276.6035 DIHED = 500.9027
1-4 NB = 179.6736 1-4 EEL = -2485.0146 VDWAALS = 47080.0882
EELEC = -375048.4042 EHBOND = 0.0000 RESTRAINT = 335.1163
EAMBER (non-restraint) = -329342.9377
------------------------------------------------------------------------------
NMR restraints: Bond = 0.009 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 995000 TIME(PS) = 1990.000 TEMP(K) = 301.33 PRESS = 0.0
Etot = -266962.1499 EKtot = 61853.9297 EPtot = -328816.0796
BOND = 166.0583 ANGLE = 284.1543 DIHED = 497.2094
1-4 NB = 181.2002 1-4 EEL = -2477.1317 VDWAALS = 47435.9867
EELEC = -375245.6085 EHBOND = 0.0000 RESTRAINT = 342.0516
EAMBER (non-restraint) = -329158.1312
------------------------------------------------------------------------------
NMR restraints: Bond = 0.012 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 996000 TIME(PS) = 1992.000 TEMP(K) = 298.28 PRESS = 0.0
Etot = -267560.3286 EKtot = 61227.8750 EPtot = -328788.2036
BOND = 181.5280 ANGLE = 264.8081 DIHED = 506.5929
1-4 NB = 182.3151 1-4 EEL = -2501.6675 VDWAALS = 47458.7044
EELEC = -375203.3333 EHBOND = 0.0000 RESTRAINT = 322.8488
EAMBER (non-restraint) = -329111.0524
------------------------------------------------------------------------------
NMR restraints: Bond = 0.021 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 997000 TIME(PS) = 1994.000 TEMP(K) = 299.21 PRESS = 0.0
Etot = -267524.0304 EKtot = 61418.8789 EPtot = -328942.9093
BOND = 179.4183 ANGLE = 281.5955 DIHED = 492.8216
1-4 NB = 179.7687 1-4 EEL = -2486.7785 VDWAALS = 47524.5111
EELEC = -375439.1742 EHBOND = 0.0000 RESTRAINT = 324.9282
EAMBER (non-restraint) = -329267.8375
------------------------------------------------------------------------------
NMR restraints: Bond = 0.079 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 998000 TIME(PS) = 1996.000 TEMP(K) = 299.75 PRESS = 0.0
Etot = -267256.7639 EKtot = 61530.4961 EPtot = -328787.2600
BOND = 166.0603 ANGLE = 265.0664 DIHED = 500.4068
1-4 NB = 186.1939 1-4 EEL = -2500.5728 VDWAALS = 47166.6117
EELEC = -374910.3165 EHBOND = 0.0000 RESTRAINT = 339.2902
EAMBER (non-restraint) = -329126.5502
------------------------------------------------------------------------------
NMR restraints: Bond = 0.146 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 999000 TIME(PS) = 1998.000 TEMP(K) = 299.35 PRESS = 0.0
Etot = -267309.4392 EKtot = 61447.1719 EPtot = -328756.6110
BOND = 162.8731 ANGLE = 274.9951 DIHED = 500.2849
1-4 NB = 179.5264 1-4 EEL = -2484.5405 VDWAALS = 47237.2285
EELEC = -374955.7262 EHBOND = 0.0000 RESTRAINT = 328.7478
EAMBER (non-restraint) = -329085.3588
------------------------------------------------------------------------------
NMR restraints: Bond = 0.111 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 1000000 TIME(PS) = 2000.000 TEMP(K) = 300.15 PRESS = 0.0
Etot = -267678.1936 EKtot = 61611.4141 EPtot = -329289.6077
BOND = 159.0282 ANGLE = 271.9056 DIHED = 495.5063
1-4 NB = 186.9755 1-4 EEL = -2490.3302 VDWAALS = 47501.0877
EELEC = -375743.2503 EHBOND = 0.0000 RESTRAINT = 329.4695
EAMBER (non-restraint) = -329619.0771
------------------------------------------------------------------------------
NMR restraints: Bond = 0.263 Angle = 0.000 Torsion = 0.000
===============================================================================
A V E R A G E S O V E R 1000 S T E P S
NSTEP = 1000000 TIME(PS) = 2000.000 TEMP(K) = 300.00 PRESS = 0.0
Etot = -266825.2364 EKtot = 61580.2676 EPtot = -328405.5040
BOND = 166.1485 ANGLE = 276.1358 DIHED = 496.4349
1-4 NB = 180.9564 1-4 EEL = -2489.0253 VDWAALS = 47249.8063
EELEC = -374618.5488 EHBOND = 0.0000 RESTRAINT = 332.5881
EAMBER (non-restraint) = -328738.0921
------------------------------------------------------------------------------
NMR restraints: Bond = 0.263 Angle = 0.000 Torsion = 0.000
===============================================================================
R M S F L U C T U A T I O N S
NSTEP = 1000000 TIME(PS) = 2000.000 TEMP(K) = 0.94 PRESS = 0.0
Etot = 730.0195 EKtot = 192.5457 EPtot = 702.7082
BOND = 9.8698 ANGLE = 9.3834 DIHED = 3.8579
1-4 NB = 3.0275 1-4 EEL = 9.3548 VDWAALS = 337.7788
EELEC = 938.4642 EHBOND = 0.0000 RESTRAINT = 12.4262
EAMBER (non-restraint) = 690.2820
------------------------------------------------------------------------------
NMR restraints on final step:
------------------------------------------------------------------------------
Final Restraint Analysis for coords: heat.rst7
Restraints, deviations, and energy contributions: pencut = 0.10
------------------------------------------------------------------------------
First atom Last atom curr. value target deviation penalty
------------------------------------------------------------------------------
O5' DC5 1 -- O5' DC5 13: 44.844 44.900 0.056 0.157 d 0: 0
Total distance penalty: 0.157
------------------------------------------------------------------------------
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Friday, June 16, 2017 9:31:52 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Weired behaviour during Heating
can you paste in your input file as text? I'm not sure of others on the
list, but I can't justify clicking on a link and downloading a zip file
just to see what might be going wrong in your simulation.
On Fri, Jun 16, 2017 at 10:26 AM, David Case <david.case.rutgers.edu> wrote:
> On Fri, Jun 16, 2017, Ramin Salimi wrote:
> >
> > I heated up my system but I see the temperature increasing very sharply
> > to 300k just in 1000 steps, which is weired to me for I have expected
> > that increases linearly with the nmropt option. Why is that so? was my
> > heating done correctly?
>
> When interpreted correctly, the nmropt is programming the *target*
> temperature
> profile. The relation of the actual temperature to the target temperature
> depends upon the nature of the thermostat, and the assoicated parameters
> like
> tautp or gamma_ln.
>
> >
> > It also starts at NSTEP=0 with TEMP=149.22. why? Is it not supposed to
> > start at TEMP=100K?
>
> This is a long-standing limitation of the way in which Amber randomizes
> velocities. Run short simulations with ntpr=1, and follow the temperature.
> It should go back to 100 (in this example) very quickly.
>
> >
> > #Explicit heating for 2ns although it heats up for the 1st ns only, then
> > stabilizes for the other half.
>
> I'm traveling right now, and can't look at this....maybe someone else on
> the
> list can help out.
>
> ....dac
>
>
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Received on Fri Jun 16 2017 - 11:00:02 PDT
