I don't see any immediate answer, but a few things to consider:
- don't specify the same input variable twice (like with nmropt). You'll
end up changing one and not the other and get unexpected results.
- using both positional and distance restraints at the same time can be
bad, especially if they don't both match the initial structure. There is
usually no reason to do both.
read the entire beginning of the mdout file, not just the energies part.
What does it say about your requested temperature changes? Does it look
correct?
On Fri, Jun 16, 2017 at 1:52 PM, Ramin Salimi <ramin.salimi01.utrgv.edu>
wrote:
> 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > https://na01.safelinks.protection.outlook.com/?url=
> http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%
> 2Famber&data=02%7C01%7Cramin.salimi01%40utrgv.edu%
> 7Caa714fb8cf774c1d95fb08d4b4c48757%7C990436a687df491c91249afa91f8
> 8827%7C0%7C0%7C636332203547710624&sdata=jHz2cD0z0%2B00%
> 2FSV9G261o77QIvX2qolGiYs%2Fik2K3vM%3D&reserved=0
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://na01.safelinks.protection.outlook.com/?url=
> http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%
> 2Famber&data=02%7C01%7Cramin.salimi01%40utrgv.edu%
> 7Caa714fb8cf774c1d95fb08d4b4c48757%7C990436a687df491c91249afa91f8
> 8827%7C0%7C0%7C636332203547710624&sdata=jHz2cD0z0%2B00%
> 2FSV9G261o77QIvX2qolGiYs%2Fik2K3vM%3D&reserved=0
> _______________________________________________
> 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
Received on Fri Jun 16 2017 - 12:00:02 PDT
