Re: AW: AW: CUDA problem?

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Apr 07 2012 - 00:40:04 CDT

Hi:
I have detected the bug in my files: VMD failed to remove anisou atoms
for just one peripheral aa, thus not giving very high VDW. Being far
from the metal centers, that had escaped my attention. Subsequent H
addition with REDUCE created a mess at that aa, which came to light
with MD: atoms moving too fast for that residue.

Removed those anisou, the minimization gradient (with non-cuda v.
2.9b3) ended to:

LINE MINIMIZER REDUCING GRADIENT FROM 1569.71 TO 1.56971

and min.log ended to:

ENERGY: 10000 9690.4862 7528.7320 1041.9845
55.1845 -325947.6443 40020.2185 0.0000
0.0000 0.0000 -267611.0387 0.0000
-267611.0387 -267611.0387 0.0000 2614.7207
2617.6077 554377.5341 2614.7207 2617.6077

Still, as implied from the above, cuda v. 2.9b2 led to "cuda
check_local_progress polled 1000000 times". Not with MD (heating),
where cuda v 2.9b2 behaved normally. In this case, the cuda devices
are seen by namd as;

Info: Based on Charm++/Converse 60400 for multicore-linux64-iccstatic
Info: Built Fri Mar 30 02:24:42 CDT 2012 by jim on lisboa.ks.uiuc.edu
Info: 1 NAMD CVS-2012-03-30 Linux-x86_64-multicore-CUDA 6 gig64 francesco
Info: Running on 6 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0158091 s
Pe 1 physical rank 1 will use CUDA device of pe 2
Pe 3 physical rank 3 will use CUDA device of pe 4
Pe 5 physical rank 5 will use CUDA device of pe 4
Pe 4 physical rank 4 binding to CUDA device 1 on gig64: 'GeForce GTX
580' Mem: 1535MB Rev: 2.0
Pe 2 physical rank 2 binding to CUDA device 0 on gig64: 'GeForce GTX
580' Mem: 1535MB Rev: 2.0
Did not find +devices i,j,k,... argument, using all
Pe 0 physical rank 0 will use CUDA device of pe 2
Info: 8.09766 MB of memory in use based on /proc/self/stat
Info: Configuration file is heat.conf

OS: Debian amd64 wheezy (testing). nvidia driver: 295.33, as provided by the OS.

I did not try cuda v 2.9b1.

francesco

On Fri, Apr 6, 2012 at 3:10 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>
> The minimizer seems to have stalled because the gradient and energies are
> inconsistent (which is not unusual due to numerical imprecision very near a
> minimum).  Your IMPRP and VDW energies don't look unusual compared to the
> DIHED and much larger negative ELECT energies, and it is impossible to
> simultaneously minimize VDW and ELECT, so you would expect one to increase
> as the other decreases near a minimum.  Minimization is a convergent
> process, so the energy won't drop forever.
>
> -Jim
>
>
>
> On Fri, 6 Apr 2012, 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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