AMBER Archive (2002)

Subject: Re: Pressure probs in MD

From: jim caldwell (caldwell_at_heimdal.compchem.ucsf.edu)
Date: Thu Jul 25 2002 - 10:55:57 CDT

Linmin failure simply means that the minimizer code
can't improve your structure and is giving up.
I'd recommend looking at the structure to see
if anything is obviously wrong.

Pressure is a second order effect (calculated from the energy
derivatives) and as such fluctuates much more than the energy
(temperature). Setting TauP too tight will mess up your
trajectory, only worry about the average pressure at the
end of the run.

On Thu, 25 Jul 2002, suvendu lomash wrote:

> HI !!
> I've modeled a cytosolic protein and trying to do MD
> simulation studies on it using AMBER5. I'm facing two
> problems:
> 1. I set up a water box of 216 TIP3 water molecules
> (using solvateDontClip in Xleap)& then tried to
> minimise first the solvent keeping the protein
> constrained (protein has already been minimised in
> vacuum ). This resulted in the bond, VanderWalls & EEL
> energy becoming significantly large. I've tried using
> Shake, but the Run stopped in between after about 800
> cycles, displaying "LINMIN FAILURE". I dont have the
> slightest idea about what it means or what am I
> supposed to do about it.
> 2. Since the minimisation run, nevertheless, generated
> a restart file, I proceeded with MD with constant
> pressure and protein constrained to equilibriate the
> solvent. Here, I've faced a lot of problem in
> obtaining a stable pressure. Had to tighten TAUP to
> 0.01 (manual recommends 1-5ps). Also, even though I've
> set TEMPO = 300, the temperature keeps hovering around
> 305K. How to stabilise these parameters?
>
> Following are the input & output files:
>
> #minimization
>
> &cntrl
>
> IMIN = 1,
>
> NTX = 1, IREST = 0,
>
> NTXO = 1, NTPR = 100,
>
> NTF = 1, NTB = 1, IDIEL = 1, DIELC = 1,
>
> CUT = 8.0, NSNB = 25, SCNB = 2.0, SCEE=1.2,
>
> NTR = 1, IBELLY = 0,
>
> MAXCYC = 2000, NCYC = 200, NTMIN = 1,
>
> DX0 = 0.01, DXM = 0.05, DRMS = 0.0001,
>
> NRUN = 0, INIT = 3,
>
> TEMP0=20, TEMPI= 0,
>
> &end
>
> Group 1
>
> 1.000
>
> RES 1 156
>
> END
>
> END
>
>
>
> -------------------------------------------------------------------------------
> FINAL RESULTS
>
> NSTEP ENERGY RMS GMAX
> NAME NUMBER
> 2000 -8.3194E+04 5.0185E-01 3.8746E+01
> SG 305
>
> BOND = 6569.9868 ANGLE = 404.5978
> DIHED = 840.2151
> VDWAALS = 16377.9255 EEL = -116880.0034
> HBOND = 0.0000
> 1-4 VDW = 505.5352 1-4 EEL = 8916.7494
> CONSTRAINT = 70.7141
> EAMBER = -83264.9935
>
> # If NTF = 3 ; NTC = 3 is used I get :
>
> FINAL RESULTS
> NSTEP ENERGY RMS GMAX
> NAME NUMBER
> 749 -6.0820E+04 1.4074E+01 4.5064E+01
> O 12545
>
> BOND = 0.0000 ANGLE = 436.7083
> DIHED = 868.4042
> VDWAALS = 3834.1585 EEL = -75732.8212
> HBOND = 0.0000
> 1-4 VDW = 605.7295 1-4 EEL = 9163.0613
> CONSTRAINT = 4.8569
> EAMBER = -60824.7595
>
> ***** REPEATED LINMIN FAILURE *****
>
> Next I had put the restart file from the above run in
> to MD with the following input file.
> #MD
>
> &cntrl
>
> IMIN = 0,
>
> NTX = 7, IREST = 1, NTRX = 1,
>
> NTXO = 1, NTPR = 100, NTWXM = 0,
>
> NTF = 2, NTB = 2, IDIEL = 1, DIELC = 1,
>
> CUT = 8.0, NSNB = 25, SCNB = 2.0, SCEE = 1.2,
>
> NTR = 1, IBELLY = 0,
>
> NRUN = 1, NSTLIM = 1000,
>
> NDFMIN = 6, NTCM = 1, NSCM = 100, INIT = 4, DT =
> 0.002,
> TEMP0=300, TEMPI=300, NTT = 5, TAUTP = 2.0, TAUTS =
> 0.1, VLIMIT = 20.0,
> NTP = 1, NPSCAL = 1, PRES0 = 1.0, COMP =44.6,
> TAUP = 0.01,
> NTC = 2, TOL = 0.0005,
>
> IMGSLT = 1,
>
> &end
>
> Group 1
>
> 1.000
>
> RES 1 156
>
> END
>
> END
>
> #output at 100ps of solvent equilibriation
> NSTEP = 500 TIME(PS) = 100.000 TEMP(K) =
> 306.06 PRESS = -13.56
> Etot = -50496.5096 EKtot = 13891.6135 EPtot
> = -64388.1231
> BOND = 457.5937 ANGLE = 1289.0477 DIHED
> = 1044.3666
> 1-4 NB = 579.0341 1-4 EEL = 8903.8669
> VDWAALS = 8439.7900
> EELEC = -85333.4539 EHBOND = 0.0000
> CONSTRAINT = 231.6318
> EAMBER (non-constraint) = -64619.7549
> EKCMT = 5949.0999 VIRIAL = 6014.6332 VOLUME
> = 223779.1841
> T_SOLUTE = 312.0014 T_SOLVENT = 305.1337
>
> Density = 1.0106
>
> ------------------------------------------------------------------------------
>
> RESULT OF LEAST SQUARE FIT OVER 100 STEPS
> ENERGY DRIFT PER STEP = 0.482713
> ETOT(AT X=0) = -5.050E+04
> NB-update: NPAIRS = 2947114 HBPAIR = 881596
> NB-update: NPAIRS = 2950392 HBPAIR = 883136
> NB-update: NPAIRS = 2952518 HBPAIR = 882360
> NB-update: NPAIRS = 2948627 HBPAIR = 881576
>
> NSTEP = 600 TIME(PS) = 100.200 TEMP(K) =
> 300.44 PRESS = 18.89
> Etot = -50483.7521 EKtot = 13636.3004 EPtot
> = -64120.0525
> BOND = 476.0253 ANGLE = 1341.7558 DIHED
> = 1058.1273
> 1-4 NB = 582.5088 1-4 EEL = 8896.3333
> VDWAALS = 8394.1504
> EELEC = -85103.2590 EHBOND = 0.0000
> CONSTRAINT = 234.3054
> EAMBER (non-constraint) = -64354.3579
> EKCMT = 5797.7807 VIRIAL = 5706.4556 VOLUME
> = 223882.0072
> T_SOLUTE = 305.0666 T_SOLVENT = 299.7129
>
> Density = 1.0101
>
> ------------------------------------------------------------------------------
>
> A V E R A G E S O V E R 1000 S T E P S
> NSTEP = 1000 TIME(PS) = 101.000 TEMP(K) =
> 305.10 PRESS = 1.73
> Etot = -50477.5774 EKtot = 13847.8916 EPtot
> = -64325.4690
> BOND = 449.7897 ANGLE = 1303.5053 DIHED
> = 1053.4361
> 1-4 NB = 580.0433 1-4 EEL = 8906.4369
> VDWAALS = 8370.4212
> EELEC = -85220.0855 EHBOND = 0.0000
> CONSTRAINT = 230.9839
> EAMBER (non-constraint) = -64556.4529
> EKCMT = 5923.5515 VIRIAL = 5915.2117 VOLUME
> = 223540.3806
> T_SOLUTE = 309.2204 T_SOLVENT = 304.4540
>
> Density = 1.0116
>
> ------------------------------------------------------------------------
>
> Although on average it remains near the set point, it
> fluctuates in the intermediate steps.
> If I increase the value of TAUP to 0.5, it fluctuates
> even more.
>
> PLEASE HELP me sort these out.
> Thank you
> Suvendu
>
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James W. Caldwell (voice) 415-476-8603
Department of Pharmaceutical Chemistry (fax) 415-502-1411
Mail Stop 0446 (email) caldwell_at_heimdal.ucsf.edu
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University of California
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