[AMBER] SolvateOct box volume and cubic box information

From: Umesh Roy <umesh24crp.gmail.com>
Date: Wed, 4 Aug 2021 01:24:48 +0530

Dear Developers and Users,
         I'm a beginner in this field. I have two general questions
regarding the volume of the box provided by tleap and its connection to the
box information saved in the parameter-topology file.

I prepared a protein-water system using tleap. I have used the Amber20
version. I solvated the protein using a truncated octahedron box type. A
part of the leap.log file is added below:

> solvateOct protein TIP3PBOX 10
Scaling up box by a factor of 1.369221 to meet diagonal cut criterion
  Solute vdw bounding box: 44.481 28.560 29.343
  Total bounding box for atom centers: 71.866 71.866 71.866
      (box expansion for 'iso' is 62.7%)
  Solvent unit box: 18.774 18.774 18.774
The number of boxes: x= 4 y= 4 z= 4
  *Volume: 193437.518 A^3 (oct)*
  Total mass 102324.184 amu, Density 0.878 g/cc
  Added 5310 residues.

>From the above information, I can see the volume of the octahedron box
is *193437.518
A^3. *However, when I look into the parameter-topology file I got the
following info (a part of the parameter-topology file is added):

  1.09471219E+02 *6.31036082E+01 6.31036082E+01 6.31036082E+01*
Here I got a cubic box dimension of equal length (marked in bold).

Question 1: What is the connection between the cubic box dimension and
volume of the octahedron box?

When I started my simulation, I got the following box information from the
MD output file (A part of the output is added here):

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme =
     vdwmeth = 1, eedmeth = 1, netfrc = 1
* Box X = 63.104 Box Y = 63.104 Box Z = 63.104*
     Alpha = 109.471 Beta = 109.471 Gamma = 109.471
     NFFT1 = 64 NFFT2 = 64 NFFT3 = 64
     Cutoff= 10.000 Tol =0.100E-04
     Ewald Coefficient = 0.27511
     Interpolation order = 4

This means that box information saved in the topology file is used for the
subsequent/production run.

Question 2: Since I solvated my protein with octahedron box type. I can't
understand why I am getting cubic box information?

Any suggestions from the amber community would be highly appreciated.

Thank you.

With best regards

Umesh Roy

School of Computational and Integrative Sciences,
JNU, NEW Delhi, 110067, INDIA
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Received on Tue Aug 03 2021 - 13:00:02 PDT
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