helpAdun - Support: sr #1845, spherical cavity

Show feedback again

sr #1845: spherical cavity

Submitted by:  None
Submitted on:  Mon Dec 17 18:15:09 2007  
Category: NonePriority: 5 - Normal
Severity: 3 - NormalStatus: None
Privacy: PublicAssigned to: None
Originator Email: -unavailable-Open/Closed: Open
Operating System: None

Add a New Comment (Rich MarkupRich Markup):

You are not logged in

Please log in, so followups can be emailed to you.


Tue Dec 18 16:23:01 2007, comment #5:

Unfortunately Adun was built to solvate systems itself and therefore SCAAS was built to operate on such systems. This was necessary so individual pieces of the entire system could be treated independently (extremely useful for complicated biochemical algorithms). But, at the moment, to do this requires the user to specify each piece and for Adun to put it together.

In the future it should be possible to specify an entire collection of molecules and tell Adun how to split it up but this will have to wait.

The same with SCAAS - It could be modified to handle things differently e.g. let the user explicitly set parameters, but with all the things that need doing now it will be a while.

Basically because there are so many components, with more coming, I'm trying to restrict the user options a bit because otherwise things could start become very difficult to track and handle.

Michael Johnston <mjohnston>
Project Administrator
Tue Dec 18 16:01:18 2007, comment #4:

I was just about to post when I saw your message. After messing around with the menus for a while I understood whats going on. So the cavity objecs are used to create a solvent box... (as you say in your post). I also fount that SCASS boundry termm...

Does the SCASS boundry need a cavity object to work? Because my system is already solvated and I'm unsure how to tell SCASS where the boundry for my system is...

The sample templates are very usefull I had forgotten about them...

Tue Dec 18 15:29:15 2007, comment #3:

Nope - Cavity simple means a defined volume in space e.g. a sphere, cube, ellipsoid etc.

If you check the QuickStartFiles you'll see an explicit template, which does a basic explicit water simulation. You can export it from the interface as a AdunCore template once you've imported it - its probably the best way to see how its put together.

Basically you need
- A cavity - A volume of space with a defined space
- A container - something that takes a single data source e.g. a water molecule and replicated it around the cavity. This is then used as a data source itself.

These two give you e.g. a sphere full of waters.
The forces applied to anything are defined by the force-field and its terms.
To apply boundary conditions to the container system so the waters don't float away you have to add an extra term to the force-field that operates on it.

Thats where the SCAAS custom term comes in - it applies SCAAS boundary conditions to the system it acts on.

I find putting a template together via the interface easier than doing it by hand - it displays all the available components and what they do etc. and checks them for you.

Michael Johnston <mjohnston>
Project Administrator
Tue Dec 18 12:48:13 2007, comment #2:

So by cavity you mean that there is a potential applied at the surface?

I have tried a dynamics run with a spherical cavity but my waters keep going out. I think I doing something wrong... Here is the template:

checkpoint = {
configuration = 1000;
energy = 100;
energyDump = 1000;
externalObjects = {
metadata = {
simulationName = Output;
objectTemplates = {
configurationGenerator = {
Class = AdSimulator;
checkFPErrorInterval = 1000;
components = (
forceFields = forceFieldCollection;
numberOfSteps = 100000;
systems = systemCollection;
timeStep = 0.5;
enzymix1 = {
Class = AdEnzymixForceField;
customTerms = {
nonbondedTerm = pureNonbondedTerm1;
system = system1;
forceFieldCollection = {
Class = AdForceFieldCollection;
forceFields = (
langevinThermostat1 = {
Class = AdLangevinThermostat;
gamma = 0.005;
seed = 889;
targetTemperature = 300;
pureNonbondedTerm1 = {
Class = AdPureNonbondedTerm;
cutoff = 12;
permittivity = 1;
system = system1;
updateInterval = 20;
sphericalCavity1 = {
Class = AdSphericalBox;
centre = (
radius = 25;
system1 = {
Class = AdSystem;
centre = (
dataSource = system;
initialTemperature = 300;
removeTranslationalDOF = YES;
systemCollection = {
Class = AdSystemCollection;
systems = (

Raul Alcantara <rulix>
Mon Dec 17 19:27:11 2007, comment #1:

Not exactly sure what you mean here - The cavity defines the volume you want to fill with water.

For a standard explicit solvent calculation it needs to be big enough to contain all the protein + have the boundaries a sufficient distance from the surface of the molecule.
Sufficient really depends on your needs e.g a more exact simulation means more simulation time, but maybe a more approximate quicker simulation is enough.

The whole question of how exactly to model the solvent e.g. amount of solvent, long-range interactions, cutoffs, exact boundary conditions, is quite complicated unfortunately. Jordi should be able to illuminate you more on this.

Currently in Adun I would say around 8-10 angstroms from the sphere surface to the protein with GRF (problems with this notwithstanding) and a 14 angstrom cutoff (protein-water) is fairly good. (Adun still needs work in the area of long-range interactions).

Michael Johnston <mjohnston>
Project Administrator
Mon Dec 17 18:15:09 2007, original submission:

What is the proper way of using the spherical cavity? Should it be large enough to have all water molecules in it? or should it be declared in such a way as to get a water layer outside the cavity?




(Note: upload size limit is set to 1024 kB, after insertion of the required escape characters.)

Attach File(s):

No files currently attached


Depends on the following items: None found

Items that depend on this one: None found


Carbon-Copy List
  • -unavailable- added by mjohnston (Posted a comment)
  • -unavailable- added by rulix (Updated the item)

    Do you think this task is very important?
    If so, you can click here to add your encouragement to it.
    This task has 0 encouragements so far.

    Only logged-in users can vote.


    Error: not logged in



    Follows 1 latest change.

    Date Changed By Updated Field Previous Value => Replaced By
    Mon Dec 17 18:16:41 2007rulixOriginator Email=>-unavailable-
    Show feedback again

    Back to the top

    Powered by Savane 3.1-cleanup