AW: AW: AW: CUDA problem?

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Apr 11 2012 - 01:07:16 CDT

Of course the error cannot occur here. It's related to the gpu stuff.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Albert
> Gesendet: Freitag, 6. April 2012 14:39
> An: Francesco Pietra; Francesco Pietra; namd-l_at_ks.uiuc.edu
> Betreff: Re: AW: AW: namd-l: CUDA problem?
>
> hello:
>
> here is my log and I think with non-cuda, the minimization goes
> well:
>
>
>
> ENERGY: 9990 6076.8951 6641.4338 7651.7002
> 55.3422 -208798.7611 16034.3467 0.0000
> 22.7461 0.0000 -172316.2969 0.0000
> -172316.2969 -172316.2969 0.0000 -2751.5067
> -2760.3487 593110.5555 -2751.5067 -2760.3487
>
> LINE MINIMIZER BRACKET: DX 0.000116279 0.00010365 DU -0.1493 0.118129
> DUDX -2585.91 11.3695 2326.51
> ENERGY: 9991 6076.8569 6641.4126 7651.6998
> 55.3500 -208798.6868 16034.3254 0.0000
> 22.7459 0.0000 -172316.2961 0.0000
> -172316.2961 -172316.2961 0.0000 -2751.4834
> -2760.3142 593110.5555 -2751.4834 -2760.3142
>
> LINE MINIMIZER BRACKET: DX 1.16279e-05 0.00010365 DU -0.000775158
> 0.118129 DUDX -248.332 11.3695 2326.51
> ENERGY: 9992 6076.8912 6641.4317 7651.7002
> 55.3430 -208798.7537 16034.3446 0.0000
> 22.7461 0.0000 -172316.2970 0.0000
> -172316.2970 -172316.2970 0.0000 -2751.5043
> -2760.3453 593110.5555 -2751.5043 -2760.3453
>
> LINE MINIMIZER BRACKET: DX 1.04651e-05 1.16279e-06 DU -0.000842925
> 6.77668e-05 DUDX -248.332 -14.6015 11.3695
> ENERGY: 9993 6076.8916 6641.4319 7651.7002
> 55.3429 -208798.7544 16034.3448 0.0000
> 22.7461 0.0000 -172316.2969 0.0000
> -172316.2969 -172316.2969 0.0000 -2751.5044
> -2760.3455 593110.5555 -2751.5044 -2760.3455
>
> LINE MINIMIZER BRACKET: DX 1.04651e-05 1.16481e-07 DU -0.000842925
> 7.84995e-05 DUDX -248.332 -14.6015 -12.0018
> ENERGY: 9994 6076.8912 6641.4317 7651.7002
> 55.3430 -208798.7537 16034.3446 0.0000
> 22.7461 0.0000 -172316.2970 0.0000
> -172316.2970 -172316.2970 0.0000 -2751.5043
> -2760.3453 593110.5555 -2751.5043 -2760.3453
>
> LINE MINIMIZER REDUCING GRADIENT FROM 4625.04 TO 4.62504
> ENERGY: 9995 6079.5796 6642.0233 7651.5411
> 55.3408 -208803.0093 16034.6699 0.0000
> 22.7501 0.0000 -172317.1046 0.0000
> -172317.1046 -172317.1046 0.0000 -2755.9541
> -2760.1986 593110.5555 -2755.9541 -2760.1986
>
> ENERGY: 9996 6082.4662 6642.6954 7652.0333
> 55.3584 -208807.2713 16035.0258 0.0000
> 22.7541 0.0000 -172316.9380 0.0000
> -172316.9380 -172316.9380 0.0000 -2760.5698
> -2760.0597 593110.5555 -2760.5698 -2760.0597
>
> LINE MINIMIZER BRACKET: DX 0.000278591 0.000278591 DU -0.807588
> 0.166576
> DUDX -4625.04 -1149.83 2330.75
> ENERGY: 9997 6080.5072 6642.2355 7651.6311
> 55.3444 -208804.4058 16034.7836 0.0000
> 22.7514 0.0000 -172317.1526 0.0000
> -172317.1526 -172317.1526 0.0000 -2757.4503
> -2760.1482 593110.5555 -2757.4503 -2760.1482
>
> LINE MINIMIZER BRACKET: DX 9.16412e-05 1.8695e-06 DU -0.0480941
> 0.000182354 DUDX -1149.83 -5.51214 17.8342
> colvars: Writing the state file
> "step6.1_equilibration_a.restart.colvars.state".
> colvars: Synchronizing (emptying the buffer of) trajectory file
> "step6.1_equilibration_a.colvars.traj".
> colvars: Saving collective variables state to
> "step6.1_equilibration_a.colvars.state".
> TIMING: 10000 CPU: 646.118, 0.0625219/step Wall: 646.118,
> 0.0625219/step, 0 hours remaining, 1574.234375 MB of memory in use.
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> POTENTIAL TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 10000 6080.5072 6642.2355 7651.6311
> 55.3444 -208804.4058 16034.7836 0.0000
> 22.7514 0.0000 -172317.1527 0.0000
> -172317.1527 -172317.1527 0.0000 -2757.4503
> -2760.1482 593110.5555 -2757.4503 -2760.1482
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 10000
> OPENING COORDINATE DCD FILE
> WRITING COORDINATES TO DCD FILE AT STEP 10000
> WRITING COORDINATES TO RESTART FILE AT STEP 10000
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 10000
> FINISHED WRITING RESTART VELOCITIES
> TCL: Setting parameter numsteps to 90000000
> TCL: Original numsteps 90000000 will be ignored.
> TCL: Running for 2000000 steps
> REASSIGNING VELOCITIES AT STEP 10000 TO 310 KELVIN.
> colvars: Writing the state file
> "step6.1_equilibration_a.restart.colvars.state".
> colvars: Synchronizing (emptying the buffer of) trajectory file
> "step6.1_equilibration_a.colvars.traj".
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> POTENTIAL TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 10000 462.8811 3364.7139 7651.6267
> 55.2352 -190736.0997 15641.0026 0.0000
> 22.7514 38451.3013 -125086.5876 310.9040
> -163537.8889 -125091.9321 310.9040 643.6379
> 658.7199 593110.5555 643.6379 658.7199
>
> colvars: Writing the state file
> "step6.1_equilibration_a.restart.colvars.state".
> colvars: Synchronizing (emptying the buffer of) trajectory file
> "step6.1_equilibration_a.colvars.traj".
> Info: Initial time: 24 CPUs 0.0539571 s/step 0.624504 days/ns 1574.23
> MB
> memory
> colvars: Writing the state file
> "step6.1_equilibration_a.restart.colvars.state".
> colvars: Synchronizing (emptying the buffer of) trajectory file
> "step6.1_equilibration_a.colvars.traj".
> Info: Initial time: 24 CPUs 0.05284 s/step 0.611574 days/ns 1574.23 MB
> memory
>
>
>
> On 04/06/2012 09:59 AM, Francesco Pietra wrote:
> > Hi:
> > I wonder whether normal completion of minimization with no-cuda namd
> > reported by Albert means successful minimization.
> >
> >
> > I have now also tried Linux-x86_64-multicore (64-bit Intel/AMD single
> > node), with the same files used beforewith the cuda 2.8 and 2.9b2
> > versions. The requested 10,000 steps were completed without error
> > messages, however there was no minimization at all, as shown by the
> > starting and ending log below:
> >
> > TCL: Minimizing for 10000 steps
> > ETITLE: TS BOND ANGLE DIHED
> > IMPRP ELECT VDW BOUNDARY
> MISC
> > KINETIC TOTAL TEMP POTENTIAL
> > TOTAL3 TEMPAVG PRESSURE GPRESSURE
> > VOLUME PRESSAVG GPRESSAVG
> >
> > ENERGY: 0 131511.9006 15951.4182 1089.1031
> > 80.7094 -208755.0384 69052471.1297 0.0000
> > 0.0000 0.0000 68992349.2227 0.0000
> > 68992349.2227 68992349.2227 0.0000 28546289.9186
> > 28560982.4534 672033.8185 28546289.9186 28560982.4534
> >
> > MINIMIZER SLOWLY MOVING 192 ATOMS WITH BAD CONTACTS DOWNHILL
> > ENERGY: 1 131687.0782 15972.6729 1093.8588
> > 82.4127 -208979.1378 4016972.9223 0.0000
> > 0.0000 0.0000 3956829.8071 0.0000
> > 3956829.8071 3956829.8071 0.0000 1640862.7514
> > 1655451.5178 672033.8185 1640862.7514 1655451.5178
> >
> > MINIMIZER SLOWLY MOVING 103 ATOMS WITH BAD CONTACTS DOWNHILL
> > ENERGY: 2 131746.9427 15987.1900 1096.4212
> > 85.2803 -209095.4978 451409.8409 0.0000
> > 0.0000 0.0000 391230.1773 0.0000
> > 391230.1773 391230.1773 0.0000 165310.8297
> > 179644.2803 672033.8185 165310.8297 179644.2803
> > ...............................
> > ...............................
> >
> > LINE MINIMIZER BRACKET: DX 1.88138e-301 3.76275e-301 DU -4.19171e-06
> > 8.16787e-06 DUDX 1.22061e+06 1.22061e+06 1.22061e+06
> > ENERGY: 9996 121119.4585 15410.7498 1102.0830
> > 129.7461 -213732.3772 18984.3934 0.0000
> > 0.0000 0.0000 -56985.9464 0.0000
> > -56985.9464 -56985.9464 0.0000 -14603.1699
> > -621.2528 672033.8185 -14603.1699 -621.2528
> >
> > LINE MINIMIZER BRACKET: DX 1.88138e-302 3.76275e-301 DU -1.14297e-05
> > 8.16787e-06 DUDX 1.22061e+06 1.22061e+06 1.22061e+06
> > ENERGY: 9997 121119.4585 15410.7498 1102.0830
> > 129.7461 -213732.3772 18984.3934 0.0000
> > 0.0000 0.0000 -56985.9464 0.0000
> > -56985.9464 -56985.9464 0.0000 -14603.1699
> > -621.2528 672033.8185 -14603.1699 -621.2528
> >
> > LINE MINIMIZER BRACKET: DX 1.88138e-303 3.76275e-301 DU -4.75305e-05
> > 8.16787e-06 DUDX 1.22061e+06 1.22061e+06 1.22061e+06
> > ENERGY: 9998 121119.4585 15410.7498 1102.0830
> > 129.7461 -213732.3771 18984.3934 0.0000
> > 0.0000 0.0000 -56985.9464 0.0000
> > -56985.9464 -56985.9464 0.0000 -14603.1699
> > -621.2528 672033.8185 -14603.1699 -621.2528
> >
> > LINE MINIMIZER BRACKET: DX 1.88138e-304 3.76275e-301 DU -5.37204e-05
> > 8.16787e-06 DUDX 1.22061e+06 1.22061e+06 1.22061e+06
> > ENERGY: 9999 121119.4585 15410.7498 1102.0830
> > 129.7461 -213732.3772 18984.3934 0.0000
> > 0.0000 0.0000 -56985.9464 0.0000
> > -56985.9464 -56985.9464 0.0000 -14603.1700
> > -621.2528 672033.8185 -14603.1700 -621.2528
> >
> > LINE MINIMIZER BRACKET: DX 1.88138e-305 3.76275e-301 DU -2.59996e-06
> > 8.16787e-06 DUDX 1.22061e+06 1.22061e+06 1.22061e+06
> > TIMING: 10000 CPU: 1566.85, 0.153887/step Wall: 1566.85,
> > 0.153887/step, 0 hours remaining, 514.656250 MB of memory in use.
> > ETITLE: TS BOND ANGLE DIHED
> > IMPRP ELECT VDW BOUNDARY
> MISC
> > KINETIC TOTAL TEMP POTENTIAL
> > TOTAL3 TEMPAVG PRESSURE GPRESSURE
> > VOLUME PRESSAVG GPRESSAVG
> >
> > ENERGY: 10000 121119.4585 15410.7498 1102.0830
> > 129.7461 -213732.3772 18984.3934 0.0000
> > 0.0000 0.0000 -56985.9464 0.0000
> > -56985.9464 -56985.9464 0.0000 -14603.1699
> > -621.2528 672033.8185 -14603.1699 -621.2528
> >
> > WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 10000
> > WRITING COORDINATES TO RESTART FILE AT STEP 10000
> > FINISHED WRITING RESTART COORDINATES
> > WRITING VELOCITIES TO RESTART FILE AT STEP 10000
> > FINISHED WRITING RESTART VELOCITIES
> > WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 10000
> > WRITING COORDINATES TO OUTPUT FILE AT STEP 10000
> > WRITING VELOCITIES TO OUTPUT FILE AT STEP 10000
> > ====================================================
> >
> > WallClock: 1592.629395 CPUTime: 1592.629395 Memory: 514.656250 MB
> > Program finished.
> >
> > *************
> > The gradient:
> >
> > LINE MINIMIZER REDUCING GRADIENT FROM 4.52147e+08 TO 452147
> > MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
> > LINE MINIMIZER REDUCING GRADIENT FROM 4.54669e+08 TO 454669
> > ......................
> > ......................
> > MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
> > LINE MINIMIZER REDUCING GRADIENT FROM 4.54669e+08 TO 454669
> > LINE MINIMIZER REDUCING GRADIENT FROM 4.54669e+08 TO 454669
> > LINE MINIMIZER REDUCING GRADIENT FROM 4.54665e+08 TO 454665
> > LINE MINIMIZER REDUCING GRADIENT FROM 4.54509e+08 TO 454509
> > LINE MINIMIZER REDUCING GRADIENT FROM 4.54096e+08 TO 454096
> >
> > scores very badly, i.e., the minimizer was unable to deal with a
> badly
> > parameterized system.
> >
> > I wonder whether Albert got the cuda error along a successful
> minimization.
> >
> > In my case, the two metal clusters reproduce nicely the crystal data
> > and min-restart-coor after the attemped 10,000 step minimization do
> > not show any wrong structural element at the naked eye. The ensemble
> > is in a water box, which also does not show distortions. I was using
> > 0.1fs ts and overall a min.conf that was successful in all previous
> > cases of metalloproteins parameterized at home.
> >
> > My question was, and remains, how to get a clue abot atom-atom
> > interactions that may explain the high (and un-minimizable) VDW and
> > IMPR. My naive view is that once that adjustment in the input files
> is
> > done, neither no-cuda, nor cuda will show problems any more. I regret
> > to be unable to furnish more elements for debugging, however the
> > software is not helping me by showing flying out atoms.
> >
> > Thanks for advice
> >
> > francesco
> >
> > On Fri, Apr 6, 2012 at 5:37 AM, Jim Phillips<jim_at_ks.uiuc.edu> wrote:
> >> This is the real error:
> >>
> >> FATAL ERROR: cuda_check_remote_progress polled 1000000 times over
> 101.085352
> >> s on step 1778
> >>
> >> What it means is that NAMD has been waiting 101s for the CUDA event
> >> indicating that the kernel has completed and NAMD is exiting rather
> than
> >> likely hanging indefinitely. I've noticed that these errors were
> more
> >> likely with energy evaluation (hence the connection to
> minimization),
> >> certain compiler settings (-ftz), and particular devices on the
> Forge
> >> cluster at NCSA that later crashed, suggesting this this is some
> kind of
> >> hardware issue (GPU or PCIe bus) or driver/runtime/compiler fault.
> The
> >> alternative is that I've missed a race condition that leads to an
> infinite
> >> loop in the kernel.
> >>
> >> I'm really hoping someone will find a way to trigger this
> consistently since
> >> in my experience it has been too rare to identify a cause.
> >>
> >> -Jim
> >>
> >>
> >> On Thu, 5 Apr 2012, Norman Geist wrote:
> >>
> >>> I guess the developers will fix this soon as 2.9b2 is a beta, bugs
> are
> >>> expected. And reports a wished.
> >>>
> >>>
> >>>
> >>> Norman Geist.
> >>>
> >>>
> >>>
> >>> Von: Albert [mailto:mailmd2011_at_gmail.com]
> >>> Gesendet: Donnerstag, 5. April 2012 08:16
> >>> An: Norman Geist; namd-l_at_ks.uiuc.edu
> >>> Betreff: Re: AW: namd-l: CUDA problem?
> >>>
> >>>
> >>>
> >>> Hello:
> >>> thank you very much for kind messages.
> >>> Is there an solution for this problem?
> >>>
> >>> best
> >>> A
> >>>
> >>> On 04/05/2012 08:12 AM, Norman Geist wrote:
> >>>
> >>> Hi,
> >>>
> >>>
> >>>
> >>> there seems to be something wrong within the new gpu accelerated
> >>> minimization as Francesco posted the same issue and I answered him
> a few
> >>> second ago. I first thought this could also be an hardware issue of
> a single
> >>> gpu, but two people with a broken gpu is really unlikely. So it’s
> the
> >>> developers turn.
> >>>
> >>>
> >>>
> >>> Best wishes
> >>>
> >>>
> >>>
> >>> Norman Geist.
> >>>
> >>>
> >>>
> >>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag
> >>> von Albert
> >>> Gesendet: Mittwoch, 4. April 2012 21:03
> >>> An: namd-l_at_ks.uiuc.edu
> >>> Betreff: namd-l: CUDA problem?
> >>>
> >>>
> >>>
> >>> Dear:
> >>> I've built a membrane system from CHARMM GUI and use the
> equilibration
> >>> protocol to relax my system. Everything goes well if I use the
> default
> >>> setting and it was finished under CUDA mode. However, there is a
> ligand in
> >>> my system and I would like to restrain it during step 6.1(see below
> of the
> >>> file). Here is what I did to add constrain for my ligand
> >>>
> >>> set sel [atomselect top all]
> >>> $sel set beta 0
> >>> set fix [atomselect top "protein and backbone or (resname LIG and
> not
> >>> hydrogen)"]
> >>> $fix set beta 1
> >>> $sel writepdb bb_rmsd.ref
> >>>
> >>>
> >>>
> >>> after that I am trying to run this 6.1.inp by command:
> >>>
> >>> charmrun ++local +p4 namd2 +idlepoll step6.1_equilibration.inp>
> log
> >>>
> >>>
> >>>
> >>>
> >>> a few minutes later, it stopped with following logs:
> >>>
> >>>
> >>> ---------log----------------
> >>> LINE MINIMIZER BRACKET: DX 7.96611e-05 0.000159322 DU -84.715
> 50.7203 DUDX
> >>> -1.52698e+06 -592619 1.21989e+06
> >>> ENERGY: 1776 5819.8403 10258.1721 9471.5998 94.8591 -182114.5405
> >>> 16169.6595 0.0000 3.2133 0.0000 -140297.1965 0.0000 -140297.1965
> >>> -140297.1965 0.0000 3492.2283 3770.7578 593110.5555 3492.2283
> 3770.7578
> >>>
> >>> LINE MINIMIZER BRACKET: DX 5.18225e-05 0.0001075 DU -15.3777 66.098
> DUDX
> >>> -592619 3098.88 1.21989e+06
> >>> ENERGY: 1777 5817.4042 10259.2760 9467.1949 94.8526 -182109.7937
> >>> 16170.7783 0.0000 3.2124 0.0000 -140297.0753 0.0000 -140297.0753
> >>> -140297.0753 0.0000 3495.3068 3772.9724 593110.5555 3495.3068
> 3772.9724
> >>>
> >>> LINE MINIMIZER BRACKET: DX 5.18225e-06 0.0001075 DU -0.121147
> 66.098 DUDX
> >>> -56148.6 3098.88 1.21989e+06
> >>> ------------- Processor 2 Exiting: Called CmiAbort ------------
> >>> Reason: FATAL ERROR: cuda_check_remote_progress polled 1000000
> times over
> >>> 101.085352 s on step 1778
> >>>
> >>> FATAL ERROR: cuda_check_remote_progress polled 1000000 times over
> >>> 101.085352 s on step 1778
> >>> Charm++ fatal error:
> >>> FATAL ERROR: cuda_check_remote_progress polled 1000000 times over
> >>> 101.085352 s on step 1778
> >>>
> >>>
> >>> However, if I don't use CUDA mode, everthing goes well.... and the
> >>> simulation can be finished without any error.... Would you please
> give me
> >>> some advices for this?
> >>>
> >>>
> >>> ----------step 6.1.inp-------------
> >>> structure ../step5_assembly.xplor_ext.psf
> >>> coordinates ../step5_assembly.pdb
> >>>
> >>> set temp 310;
> >>> set outputname step6.1_equilibration;
> >>>
> >>> # read system values written by CHARMM (need to convert uppercases
> to
> >>> lowercases)
> >>> exec tr "\[:upper:\]" "\[:lower:\]"< ../step5_assembly.str | sed -
> e "s/ =
> >>> //g"> step5_assembly.namd.str
> >>> source step5_assembly.namd.str
> >>>
> >>> temperature $temp;
> >>>
> >>> outputName step6.1_equilibration_a; # base name for output from
> this run
> >>> # NAMD writes two files at the end, final coord and vel
> >>> # in the format of first-dyn.coor and first-dyn.vel
> >>> firsttimestep 0; # last step of previous run
> >>> restartfreq 500; # 500 steps = every 1ps
> >>> dcdfreq 1000;
> >>> dcdUnitCell yes; # the file will contain unit cell info in the
> style of
> >>> # charmm dcd files. if yes, the dcd files will contain
> >>> # unit cell information in the style of charmm DCD files.
> >>> xstFreq 1000; # XSTFreq: control how often the extended systen
> >>> configuration
> >>> # will be appended to the XST file
> >>> outputEnergies 125; # 125 steps = every 0.25ps
> >>> # The number of timesteps between each energy output of NAMD
> >>> outputTiming 1000; # The number of timesteps between each timing
> output
> >>> shows
> >>> # time per step and time to completion
> >>>
> >>> # Force-Field Parameters
> >>> paraTypeCharmm on; # We're using charmm type parameter file(s)
> >>> # multiple definitions may be used but only one file per definition
> >>>
> >>> exec mkdir -p toppar
> >>> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g"
> ./toppar/par_all22_prot.prm>
> >>> toppar/par_all22_prot.prm
> >>> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g"
> ../toppar/par_all27_na.prm>
> >>> toppar/par_all27_na.prm
> >>> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g"
> ./toppar/par_all36_carb.prm>
> >>> toppar/par_all36_carb.prm
> >>> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g"
> ./toppar/par_all36_lipid.prm
> >>>> toppar/par_all36_lipid.prm
> >>> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g"
> ./toppar/par_all36_cgenff.prm
> >>>> toppar/par_all36_cgenff.prm
> >>> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" -e "1,/read para/d" \
> >>> -e "278,296d" -e "s/^BOM/!&/g" -e "s/^WRN/!&/g"
> >>> ./toppar/toppar_water_ions.str> toppar/toppar_water_ions.str
> >>> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" -e "1,/read para/d" \
> >>> -e "278,296d" -e "s/^BOM/!&/g" -e "s/^WRN/!&/g"
> >>> ./toppar/toppar_all36_lipid_cholesterol.str>
> >>> toppar/toppar_all36_lipid_cholesterol.str
> >>>
> >>> parameters toppar/par_all27_prot_na.prm;
> >>> parameters toppar/par_all36_lipid.prm;
> >>> parameters toppar/par_all22_prot.prm;
> >>> parameters toppar/par_all27_na.prm;
> >>> parameters toppar/par_all36_carb.prm;
> >>> parameters toppar/par_all36_cgenff.prm;
> >>> parameters toppar/par_all35_ethers.prm;
> >>> parameters toppar/lig.prm;
> >>>
> >>>
> >>> parameters toppar/toppar_water_ions.str;
> >>> parameters toppar/toppar_all36_lipid_cholesterol.str;
> >>>
> >>> # These are specified by CHARMM
> >>> exclude scaled1-4 # non-bonded exclusion policy to use
> >>> "none,1-2,1-3,1-4,or scaled1-4"
> >>> # 1-2: all atoms pairs that are bonded are going to be ignored
> >>> # 1-3: 3 consecutively bonded are excluded
> >>> # scaled1-4: include all the 1-3, and modified 1-4 interactions
> >>> # electrostatic scaled by 1-4scaling factor 1.0
> >>> # vdW special 1-4 parameters in charmm parameter file.
> >>> 1-4scaling 1.0
> >>> switching on
> >>> vdwForceSwitching yes; # New option for force-based switching of
> vdW
> >>> # if both switching and vdwForceSwitching are on CHARMM force
> >>> # switching is used for vdW forces.
> >>> seed 1333525265 # Specifies a specific seed
> >>>
> >>> # You have some freedom choosing the cutoff
> >>> cutoff 12.0; # may use smaller, maybe 10., with PME
> >>> switchdist 10.0; # cutoff - 2.
> >>> # switchdist - where you start to switch
> >>> # cutoff - where you stop accounting for nonbond interactions.
> >>> # correspondence in charmm:
> >>> # (cutnb,ctofnb,ctonnb = pairlistdist,cutoff,switchdist)
> >>> pairlistdist 16.0; # stores the all the pairs with in the distance
> it
> >>> should be larger
> >>> # than cutoff( + 2.)
> >>> stepspercycle 20; # 20 redo pairlists every ten steps
> >>> pairlistsPerCycle 2; # 2 is the default
> >>> # cycle represents the number of steps between atom reassignments
> >>> # this means every 20/2=10 steps the pairlist will be updated
> >>>
> >>> # Integrator Parameters
> >>> timestep 1.0; # fs/step
> >>> rigidBonds all; # Bound constraint all bonds involving H are fixed
> in
> >>> length
> >>> nonbondedFreq 1; # nonbonded forces every step
> >>> fullElectFrequency 1; # PME every step
> >>>
> >>>
> >>> # Constant Temperature Control ONLY DURING EQUILB
> >>> reassignFreq 500; # reassignFreq: use this to reassign velocity
> every 500
> >>> steps
> >>> reassignTemp $temp;
> >>>
> >>> # Periodic Boundary conditions. Need this since for a start...
> >>> cellBasisVector1 $a 0.0 0.0; # vector to the next image
> >>> cellBasisVector2 0.0 $b 0.0;
> >>> cellBasisVector3 0.0 0.0 $c;
> >>> cellOrigin 0.0 0.0 $zcen; # the *center* of the cell
> >>>
> >>> wrapWater on; # wrap water to central cell
> >>> wrapAll on; # wrap other molecules too
> >>> wrapNearest off; # use for non-rectangular cells (wrap to the
> nearest
> >>> image)
> >>>
> >>> # PME (for full-system periodic electrostatics)
> >>> exec python ../checkfft.py $a $b $c> checkfft.str
> >>> source checkfft.str
> >>>
> >>> PME yes;
> >>> PMEInterpOrder 6; # interpolation order (spline order 6 in charmm)
> >>> PMEGridSizeX $fftx; # should be close to the cell size
> >>> PMEGridSizeY $ffty; # corresponds to the charmm input fftx/y/z
> >>> PMEGridSizeZ $fftz;
> >>>
> >>> # Pressure and volume control
> >>> useGroupPressure yes; # use a hydrogen-group based pseudo-molecular
> viral
> >>> to calcualte pressure and
> >>> # has less fluctuation, is needed for rigid bonds
> (rigidBonds/SHAKE)
> >>> useFlexibleCell yes; # yes for anisotropic system like membrane
> >>> useConstantRatio yes; # keeps the ratio of the unit cell in the x-y
> plane
> >>> constant A=B
> >>>
> >>> langevin on
> >>> langevinDamping 10
> >>> langevinTemp $temp
> >>> langevinHydrogen no
> >>>
> >>> # planar restraint
> >>> colvars on
> >>> exec sed -e "s/Constant \$fc/Constant 5/g" -e "s/\$bb/10.0/g" -e
> >>> "s/\$sc/5.0/g" membrane_lipid_restraint.namd.col>
> >>> restraints/$outputname.col
> >>> colvarsConfig restraints/$outputname.col
> >>>
> >>> # dihedral restraint
> >>> extraBonds yes
> >>> exec sed -e "s/\$FC/500/g" restraints/dihe.txt>
> >>> restraints/$outputname.dihe
> >>> extraBondsFile restraints/$outputname.dihe
> >>>
> >>> minimize 10000
> >>>
> >>> numsteps 90000000
> >>> run 3000000 ; 3ns
> >>>
> >>>
> >>>

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