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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Dec 16 2009 - 02:13:59 CST

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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