VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Dec 17 2009 - 12:27:15 CST

With cell dimensions below, and geometric center from measure center
previously posted, the minimization could be carried out;

WRITING COORDINATES TO DCD FILE AT STEP 999
TIMING: 1000 CPU: 938.295, 1.08979/step Wall: 1217.42, 1.15025/step,
0 hours remaining, 28.390259 MB of memory in use.
PRESSURE: 1000 -1844.48 17.4045 -16.9614 21.1917 -1888.1 32.7878
-12.7146 27.1588 -1377.14
GPRESSURE: 1000 -1844.48 17.4045 -16.9614 21.1917 -1888.1 32.7878
-12.7146 27.1588 -1377.14
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
       KINETIC TOTAL TEMP POTENTIAL
  TOTAL3 TEMPAVG PRESSURE GPRESSURE
VOLUME PRESSAVG GPRESSAVG

ENERGY: 1000 1266.4376 3301.3237 1238.8804
0.0000 -4016.3769 -264365.6347 0.0000
0.0000 0.0000 -262575.3699 0.0000
-262575.3699 -262575.3699 0.0000 -1703.2357
-1703.2357 3934216.0000 -1703.2357 -1703.2357

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: 1246.301025 CPUTime: 965.900391 Memory: 28.372406 MB
Charmrun> Graceful exit.

I am most sorry for not having immediately recognized that the
dimensions were not inclusive of the solvation water. Now I have to
learn how to "measure" cg systems in order to treat correctly them.

francesco

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Thu, Dec 17, 2009 at 9:34 AM
Subject: Fwd: Fwd: vmd-l: Re: namd-l: Fwd: conf file for coarse
grained simulation
To: Peter Freddolino <petefred_at_ks.uiuc.edu>
Cc: vmd <vmd-l_at_ks.uiuc.edu>

In fact, on a rough graphic inspection (with Chimera, I have to learn
how to do that with VMD) the solvated cell dimensions are

x 147
y 176
z 138

My silly mistake is confirmed. Could you please correct the procedure
I used to measure the cell?

thanks
francesco

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Thu, Dec 17, 2009 at 9:05 AM
Subject: Re: Fwd: vmd-l: Re: namd-l: Fwd: conf file for coarse grained
simulation
To: Peter Freddolino <petefred_at_ks.uiuc.edu>

Hello Peter:

The cell size and center came from:

--launch VMD

--Load solvated .psf and pdb

--Tk Console

--Set all [atomselect top all]

--measure center $all
  35.1028..  46.859...  28.922...

--measure minmax $all
 {-39.891...   -43.641...   -40.103...}
 {109.567...  136.141...   98.125}

(these max values are reasonable for the non-solvated protein+bilayer;
see at the end my conclusion)

--molinfo top set a 109

--molinfo top set b 136

--molinfo top set c 98

--Graphic repres.. Periodic .. select all x -x y -y z -z
to get the posted image.

In minimize conf:
# Periodic Boundary Conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {1} {
cellBasisVector1    109.    0.   0.
cellBasisVector2     0.   136.   0.
cellBasisVector3     0.    0.  98.
cellOrigin         35.102874755859375 46.8595085144043 28.922983169555664
}
wrapWater           on
wrapAll             on

 #PME (for full-system periodic electrostatics)
if {1} {
PME                 yes
PMEGridSizeX       109
PMEGridSizeY       136
PMEGridSizeZ       98
}

=====
I did not take

 {-39.891...   -43.641...   -40.103...}

into account when using the Solvate plugin, where:

Boundary 5.0

Use molecule dimensions

Box padding 25 in all six boxes

Use nonstandard solvent
 cgwat.pdb
 cgwat.psf
 rbcg-2007.top
 side length 40
 name H2O
===

To create the .fix file:

--VMD ... Tk console

--mol load psf ...psf  pdb  ...pdb

--set all [atomselect top "all"]

$all set beta 0

--set fixed [atomselect top "protein or (chain O and name CHO PHO ES1
ES2 ME1 ME2 ME3 MT1 ME4 ME5 ME6 MT2)"]

$fixed set beta 1

$all writepdb ...fix

whereby POPC got 1.00 in beta column while the cg protein not (how
should it - and cg water - be named?). I set 1.00 in beta column for
the protein with a script.

>From your observations it seems to me now -as alluded to above - that
the method I used to pick up the cell dimensions did not take into
account the solvation water. If so, it was a most silly overlooking
because it was clear to me that the protein-bilayer is sized - more or
less -  109 136 98 A.

thanks
francesco

On Thu, Dec 17, 2009 at 1:49 AM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> 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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