Re: Fwd: vmd-l: Re: Fwd: conf file for coarse grained simulation

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Dec 16 2009 - 18:49:13 CST

Hi Francesco,
it is pretty apparent from the image that you posted that your periodic
cells overlap with each other, meaning lots and lots of clashes are
occuring. Have a look at every point where there's an interface between
images -- you get double density of water. How did you pick your
periodic cell size?
Peter

Francesco Pietra wrote:
> Forgetting about the "steepest descent" procedure, probably
> incorrectly devised, I have carefully repeated the procedure in a
> water box.
>
> First I have rebuilt the protein+bilayer model with 4.0A boundary
> between the protein and the bilayer (in previous attempts it was
> 2.4A). The protein+bilayer could be successfully minimized
> non-periodic, no PME, no restraint on any bead:
> LINE MINIMIZER BRACKET: DX 9.90228e-07 7.94702e-06 DU -0.00210952
> 0.136292 DUDX -4274.13 13.24 34182.2
> LINE MINIMIZER REDUCING GRADIENT FROM 54035.7 TO 54.0357
> WRITING COORDINATES TO DCD FILE AT STEP 999
> TIMING: 1000 CPU: 36.1463, 0.0465229/step Wall: 81.7678,
> 0.0703083/step, 0 hours remaining, 6.966660 MB of memory in use.
> PRESSURE: 1000 0 0 0 0 0 0 0 0 0
> GPRESSURE: 1000 0 0 0 0 0 0 0 0 0
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL
> TOTAL3 TEMPAVG
>
> ENERGY: 1000 1266.4280 3301.3107 1238.8463
> 0.0000 -5076.5324 -18271.7678 0.0000
> 0.0000 0.0000 -17541.7153 0.0000
> -17541.7153 -17541.7153 0.0000
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000
> WRITING COORDINATES TO DCD FILE AT STEP 1000
> WRITING COORDINATES TO RESTART FILE AT STEP 1000
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 1000
> FINISHED WRITING RESTART VELOCITIES
> REINITIALIZING VELOCITIES AT STEP 1000 TO 300 KELVIN.
> TCL: Setting parameter numsteps to 10
> WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 10
> CLOSING EXTENDED SYSTEM TRAJECTORY FILE
> WRITING COORDINATES TO OUTPUT FILE AT STEP 10
> CLOSING COORDINATE DCD FILE
> WRITING VELOCITIES TO OUTPUT FILE AT STEP 10
> ====================================================
>
> WallClock: 83.922256 CPUTime: 37.538345 Memory: 6.827713 MB
> Charmrun> Graceful exit.
>
> cg Water solvation of the minimized system was then carried out with
> Boundary 5.0A and Padding 25A (15+10). In previous attempts it was 4.0
> and 19 (15+4).
>
> Minimization was carried out under the same conditions as in previous
> runs (periodic, PME, restraint on the protein and the lipid, which
> means that no water was restrained, be that of external solvation or
> associated with POPC)
>
> The simulation halted at step 542 (out of stated 1000) with (as
> before) no warning signal. Only one processor was still active 100%
> (top monitoring). The simulation started removing clashes (between
> solvation waters, or the gap between cell is still not large enough?
> please see the attached image of the periodic cells):
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> MINIMIZER SLOWLY MOVING 18573 ATOMS WITH BAD CONTACTS DOWNHILL
> PRESSURE: 1 -1.85929e+15 -1.99318e+15 -1.13841e+15 7.73135e+13
> 2.58478e+15 -1.60992e+15 2.13888e+14 4.95167e+14 -7.73779e+13
> GPRESSURE: 1 -1.85929e+15 -1.99318e+15 -1.13841e+15 7.73135e+13
> 2.58478e+15 -1.60992e+15 2.13888e+14 4.95167e+14 -7.73779e+13
> ENERGY: 1 1266.4376 3301.3237 1238.8804
> 0.0000 -4957.8167 9999999999.9999 0.0000
> 0.0000 0.0000 9999999999.9999 0.0000
> 9999999999.9999 9999999999.9999 0.0000 9999999999.9999
> 9999999999.9999 1452752.0000 9999999999.9999 9999999999.9999
>
> MINIMIZER SLOWLY MOVING 16749 ATOMS WITH BAD CONTACTS DOWNHILL
> OPENING COORDINATE DCD FILE
> WRITING COORDINATES TO DCD FILE AT STEP 1
> PRESSURE: 2 -9.61887e+13 -9.14159e+13 -5.43871e+13 2.85652e+13
> 1.3131e+14 -6.18717e+13 1.15444e+13 2.7896e+13 -6.19013e+12
> GPRESSURE: 2 -9.61887e+13 -9.14159e+13 -5.43871e+13 2.85652e+13
> 1.3131e+14 -6.18717e+13 1.15444e+13 2.7896e+13 -6.19013e+12
> ENERGY: 2 1266.4376 3301.3237 1238.8804
> 0.0000 -4957.8167 9999999999.9999 0.0000
> 0.0000 0.0000 9999999999.9999 0.0000
> 9999999999.9999 9999999999.9999 0.0000 9999999999.9999
> 9999999999.9999 1452752.0000 9999999999.9999 9999999999.9999
>
> and continues so until step 26, than initiates conjugated gradient:
>
> MINIMIZER SLOWLY MOVING 1 ATOMS WITH BAD CONTACTS DOWNHILL
> WRITING COORDINATES TO DCD FILE AT STEP 25
> PRESSURE: 26 1.49959e+08 -7.27695e+06 -4.73455e+06 1.66896e+06
> 1.50542e+08 -215263 -1.29055e+06 -3.77079e+06 1.51917e+08
> GPRESSURE: 26 1.49959e+08 -7.27695e+06 -4.73455e+06 1.66896e+06
> 1.50542e+08 -215263 -1.29055e+06 -3.77079e+06 1.51917e+08
> ENERGY: 26 1266.4376 3301.3237 1238.8804
> 0.0000 -4957.8167 737159432.2607 0.0000
> 0.0000 0.0000 737160281.0857 0.0000
> 737160281.0857 737160281.0857 0.0000 150806192.8320
> 150806192.8320 1452752.0000 150806192.8320 150806192.8320
>
> MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
> LINE MINIMIZER REDUCING GRADIENT FROM 5.31294e+14 TO 5.31294e+11
> WRITING COORDINATES TO DCD FILE AT STEP 26
> PRESSURE: 27 9.27468e+07 75657.6 -1.68847e+06 1.54594e+06 9.48161e+07
> 768612 -1.43932e+06 -1.05566e+06 9.49739e+07
> GPRESSURE: 27 9.27468e+07 75657.6 -1.68847e+06 1.54594e+06 9.48161e+07
> 768612 -1.43932e+06 -1.05566e+06 9.49739e+07
> ENERGY: 27 1266.4376 3301.3237 1238.8804
> 0.0000 -4957.8167 463067070.1446 0.0000
> 0.0000 0.0000 463067918.9696 0.0000
> 463067918.9696 463067918.9696 0.0000 94178916.2476
> 94178916.2476 1452752.0000 94178916.2476 94178916.2476
>
> VDW energy did not improve much, until the procedure halted:
>
> WRITING COORDINATES TO DCD FILE AT STEP 542
> PRESSURE: 543 8.85604e+07 1.45427e+06 -1.39861e+06 1.69754e+06
> 9.11258e+07 841076 -1.52223e+06 -717614 9.07388e+07
> GPRESSURE: 543 8.85604e+07 1.45427e+06 -1.39861e+06 1.69754e+06
> 9.11258e+07 841076 -1.52223e+06 -717614 9.07388e+07
> ENERGY: 543 1266.4376 3301.3237 1238.8804
> 0.0000 -4957.8167 445412669.1165 0.0000
> 0.0000 0.0000 445413517.9415 0.0000
> 445413517.9415 445413517.9415 0.0000 90141654.9142
> 90141654.9142 1452752.0000 90141654.9142 90141654.9142
>
>
> Well, do you think that the Padding should be increased further, or
> that I am doing some silly mistake that has nothing to do with the gap
> between cells? I was aware of the Solvate plugin, actually I followed
> that. I have reexamined everything without being able to detect were I
> am wrong. Do you think worth while trying to restrain the water
> associated with POPC?
>
> Thanks
> francesco
>
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Wed, Dec 16, 2009 at 10:01 AM
> Subject: Fwd: vmd-l: Re: namd-l: Fwd: conf file for coarse grained simulation
> To: Axel Kohlmeyer <akohlmey_at_gmail.com>, Peter Freddolino <petefred_at_ks.uiuc.edu>
> Cc: NAMD <namd-l_at_ks.uiuc.edu>
>
>
> Attempts at minimizing under "steepest descent" ended in a crash. I
> wonder whether a suggestion may arise from the following.
>
> Modifications to the conf file:
>
> set temperature 0
>
> temperature $temperature
>
> langevin off
>
> # Minimization
> if {1} {
> velocityQuenching on
> maximumMove 1.5
> minimize 1000
> reinitvels $temperature
> }
>
> numsteps 10
>
> The log said:
> .............
> Info: Startup phase 7 took 0.0559781 s, 11.754 MB of memory in use
> Info: Startup phase 8 took 0.000222921 s, 11.8803 MB of memory in use
> Info: Finished startup at 15 s, 11.8803 MB of memory in use
>
> TCL: Minimizing for 1000 steps
> ------------- Processor 2 Exiting: Caught Signal ------------
> Signal: segmentation violation
> Suggestion: Try running with '++debug', or linking with '-memory paranoid'.
> [2] Stack Traceback:
> [0] /lib/libc.so.6 [0x7f4c538daf60]
> [1] _Z24sortEntries_mergeSort_v2RP12__sort_entryS1_i+0xba [0x5ce526]
> [2] _ZN20ComputeNonbondedUtil32calc_pair_energy_merge_fullelectEP9nonbonded+0x351a
> [0x592c2a]
> [3] _ZN20ComputeNonbondedPair7doForceEPP8CompAtomPP11CompAtomExtPP7Results+0xae4
> [0x57b04e]
> [4] _ZN16ComputePatchPair6doWorkEv+0xa7 [0x6e21a3]
> [5] _ZN11WorkDistrib12enqueueWorkAEP12LocalWorkMsg+0x16 [0x92ed3c]
> [6] _ZN19CkIndex_WorkDistrib31_call_enqueueWorkA_LocalWorkMsgEPvP11WorkDistrib+0xf
> [0x92ed23]
> [7] CkDeliverMessageFree+0x21 [0x9c2d71]
> [8] _Z15_processHandlerPvP11CkCoreState+0x509 [0x9c2365]
> [9] CsdScheduleForever+0xa5 [0xa4bcf5]
> [10] CsdScheduler+0x1c [0xa4b8f6]
> [11] _Z11master_initiPPc+0x280 [0x508ea0]
> [12] _ZN7BackEnd4initEiPPc+0x31 [0x508c19]
> [13] main+0x2f [0x5045af]
> [14] __libc_start_main+0xe6 [0x7f4c538c71a6]
> [15] _ZNSt8ios_base4InitD1Ev+0x52 [0x4ff9ea]
> Fatal error on PE 2> segmentation violation
>
>
> Thanks
> francesco
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Wed, Dec 16, 2009 at 9:13 AM
> Subject: Re: vmd-l: Re: namd-l: Fwd: conf file for coarse grained simulation
> To: Axel Kohlmeyer <akohlmey_at_gmail.com>
> Cc: NAMD <namd-l_at_ks.uiuc.edu>, Peter Freddolino <petefred_at_ks.uiuc.edu>
>
>
> Thanks a lot for what you wrote. Solvation from scratch with Boundary
> 4.0 and Padding 19 (15+4) did not help, or not fully. Minimization at
> const. volume (with protein+bilayer restrained) halted at step 532,
> out of 1000 set steps.
>
> The reason to posting now, before I continue to search the right
> avenue, is that now the VDW energy has decreased conspicuously, from
> initial
>
> MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
> PRESSURE: 3 1.5157e+10 1.03589e+10 4.97618e+09 9.72122e+08 1.2445e+10
> -5.9558e+08 -2.86152e+09 -1.00705e+10 1.38611e+09
> GPRESSURE: 3 1.5157e+10 1.03589e+10 4.97618e+09 9.72122e+08 1.2445e+10
> -5.9558e+08 -2.86152e+09 -1.00705e+10 1.38611e+09
> ENERGY: 3 1578.4243 3635.7565 1250.6257
> 0.0000 -5656.7864 9999999999.9999 0.0000
> 0.0000 0.0000 9999999999.9999 0.0000
> 9999999999.9999 9999999999.9999 0.0000 9662690638.0470
> 9662690638.0470 1332198.0000 9662690638.0470 9662690638.0470
>
> MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
> PRESSURE: 4 4.34298e+09 6.51726e+09 4.72519e+09 1.90218e+09
> 5.44552e+09 3.08174e+09 -2.88084e+07 -4.85553e+08 9.49706e+08
> GPRESSURE: 4 4.34298e+09 6.51726e+09 4.72519e+09 1.90218e+09
> 5.44552e+09 3.08174e+09 -2.88084e+07 -4.85553e+08 9.49706e+08
> ENERGY: 4 1583.3489 3638.1393 1260.5904
> 0.0000 -5655.4262 7235356386.7152 0.0000
> 0.0000 0.0000 7235357213.3676 0.0000
> 7235357213.3676 7235357213.3676 0.0000 3579402107.2727
> 3579402107.2727 1332198.0000 3579402107.2727 3579402107.2727
>
> to final
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 530
> WRITING COORDINATES TO DCD FILE AT STEP 530
> WRITING COORDINATES TO RESTART FILE AT STEP 530
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 530
> FINISHED WRITING RESTART VELOCITIES
> PRESSURE: 531 1.53654e+07 3.29332e+06 -372766 543512 1.72077e+07
> 1.39373e+06 1.05476e+06 1.19923e+06 1.78077e+07
> GPRESSURE: 531 1.53654e+07 3.29332e+06 -372766 543512 1.72077e+07
> 1.39373e+06 1.05476e+06 1.19923e+06 1.78077e+07
> ENERGY: 531 1600.1030 3648.7438 1294.4447
> 0.0000 -5651.9148 73889513.1000 0.0000
> 0.0000 0.0000 73890404.4767 0.0000
> 73890404.4767 73890404.4767 0.0000 16793614.9574
> 16793614.9574 1332198.0000 16793614.9574 16793614.9574
>
> WRITING COORDINATES TO DCD FILE AT STEP 531
> PRESSURE: 532 1.53654e+07 3.29332e+06 -372766 543512 1.72077e+07
> 1.39373e+06 1.05476e+06 1.19923e+06 1.78077e+07
> GPRESSURE: 532 1.53654e+07 3.29332e+06 -372766 543512 1.72077e+07
> 1.39373e+06 1.05476e+06 1.19923e+06 1.78077e+07
> ENERGY: 532 1600.1030 3648.7438 1294.4447
> 0.0000 -5651.9148 73889513.1000 0.0000
> 0.0000 0.0000 73890404.4767 0.0000
> 73890404.4767 73890404.4767 0.0000 16793614.9574
> 16793614.9574 1332198.0000 16793614.9574 16793614.9574
>
>
> Why the minimizer found it impossible to continue is what I am
> wondering about. I am considering:
>
> ---Before running conjugate gradient, run steepest descent (which is
> the rule in Amber). I rely on Peter's 2008 suggestion: "you can get
> something very similar by using velocityQuenching (turn on
> velocityQuenching and then use run X to run X steps). This method
> removes all velocity from all atoms at each step, which gives you a
> similar effect. See
> http://www.ks.uiuc.edu/Research/namd/2.6/ug/node29.html#8242 for more
> details."
>
> ---Increase Padding or Boundary, or both.
>
> ---Restrain also the water pertaining to the bilayer, in order to
> relax the external solvation water only (may be by setting 1.00 on col
> B for POPC water).
>
> ---Re-building protein+bilayer with a larger boundary (present model
> was built with 2.5A boundary between the protein and the bilayer, and
> could be minimized with namd under non-periodic conditions. This
> notwithstanding, may be that a larger boundary, 4.0A or so, is
> needed).
>
> That's all i can think about now.
>
> francesco
>
> On Tue, Dec 15, 2009 at 6:16 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
>> On Tue, 2009-12-15 at 17:01 +0100, Francesco Pietra wrote:
>>
>>> I forgot to ask: could you please suggest how roughly modify the
>>> parameters for cg solvation? I must have misinterpreted the analysis
>>> of inter-cell gap. In particular, the relationship between "Boundary"
>>> and "Box padding" is not clear to me.
>>>
>> please have a look at the online help of the solvate command. the
>> html file is a bit terse in that respect and should be updated.
>> also the URL pointing to the namd tutorial is off by one node...
>>
>> the boundary value is the distance between the solvent and solute.
>> the default value of 2.4 is fairly generous, but due to the increased
>> size of water (Martini rolls 4 waters into one site) and protein
>> side chain "atoms", stepping this up to, say, 4.0 might be a safe
>> choice. this can be easily rationalized from applying common sense:
>> just compare the values in an all-atom .par file to the coarse grain
>> .par file. the r2min/2 value in the CG .par file is 2.35 whereas the
>> corresponding AA values are between 1.3 and 1.8 with a few around 2.0.
>>
>> since your system was minimizing fine w/o periodicity, the default
>> might already be mostly ok for you. these values are empirical anyways.
>>
>> the padding value is how much solvent outside of min/max dimensions
>> of the solute you want to add. so, dimensions of solute _plus_
>> padding dimensions will be the new min/max of your system. AFAIK,
>> this does not include a "safety" (i.e. the equivalent of boundary for
>> inter cell distance), so i would just add that value or more to your
>> box dimensions.
>>
>> when visually checking for overlaps with PBC, you have to increase
>> the diameter of your vdw spheres (i just double them for our CMM
>> cg model).
>>
>> HTH,
>> axel.
>>
>>
>>> thanks
>>> francesco
>>>
>>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
>> Institute for Computational Molecular Science
>> College of Science and Technology
>> Temple University, Philadelphia PA, USA.
>>
>>
>>

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