PCACIC
From HP-SEE Wiki
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== General Information == | == General Information == | ||
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| - | + | * Application's name: ''Principal component analysis of the conformational interconversions in large-ring cyclodextrins'' | |
| + | * Application's acronym: ''PCACIC'' | ||
| + | * Virtual Research Community : ''Computational Chemistry Applications'' | ||
| + | * Scientific contact : ''Petko Ivanov, ivanov@bas.bg'' | ||
| + | * Technical contact : ''Petko Ivanov, ivanov@bas.bg'' | ||
| + | * Developers : ''Petko Ivanov, Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Lab. Physical Organic and Computational Chemistry'' | ||
| + | * Web site: ''Tobefilledin'' | ||
| + | |||
| + | == Short Description == | ||
| + | |||
A new class of compounds, the large-ring cyclodextrins (LR-CDs), attracted attention in recent years, and advances were marked in the study of their physicochemical properties, in spite of existing difficulties in their synthesis, isolation and purification. Since CDs consist of optically active D-glucose units, they form a pair of diastereoisomeric complexes, usually of different stability, with a racemic compound. There is, however, limited information about either the structure of the macrocycles in solution, or their complex-forming properties. | A new class of compounds, the large-ring cyclodextrins (LR-CDs), attracted attention in recent years, and advances were marked in the study of their physicochemical properties, in spite of existing difficulties in their synthesis, isolation and purification. Since CDs consist of optically active D-glucose units, they form a pair of diastereoisomeric complexes, usually of different stability, with a racemic compound. There is, however, limited information about either the structure of the macrocycles in solution, or their complex-forming properties. | ||
| + | |||
In view of the difficulties in the purification of individual large-ring cyclodextrins, molecular dynamics simulation techniques provide a useful tool to gain insight into their conformational dynamics and the complex-forming ability. Using molecular dynamics simulations as a conformational search protocol, post-processing of the simulation trajectories is carried out by: (i) the MM/GBSA (Generalized Born/Surface Area (LCPO)) methodology in order to estimate energy data, and (ii) principal component analysis (PCA), also called quasiharmonic analysis or essential dynamics method. | In view of the difficulties in the purification of individual large-ring cyclodextrins, molecular dynamics simulation techniques provide a useful tool to gain insight into their conformational dynamics and the complex-forming ability. Using molecular dynamics simulations as a conformational search protocol, post-processing of the simulation trajectories is carried out by: (i) the MM/GBSA (Generalized Born/Surface Area (LCPO)) methodology in order to estimate energy data, and (ii) principal component analysis (PCA), also called quasiharmonic analysis or essential dynamics method. | ||
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These studies require enormous computational resources. It took only about five years in order to access an order of magnitude longer duration of the simulations for these systems. This is the reason why the use of HPC is necessary. | These studies require enormous computational resources. It took only about five years in order to access an order of magnitude longer duration of the simulations for these systems. This is the reason why the use of HPC is necessary. | ||
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Previous releases of this application have been run on HPC resources of "Mare Nostrum" at the Barcelona Supercomputing Center. | Previous releases of this application have been run on HPC resources of "Mare Nostrum" at the Barcelona Supercomputing Center. | ||
== Problems Solved == | == Problems Solved == | ||
| + | |||
The LR-CDs, as the native CDs, are potential reagents for chiral resolution. With this application we can monitor the concerted motions of the atoms of the molecule in a few dimensions, making it easier to visualize and investigate these motions. Our efforts will be devoted to execute additional 50.0 ns simulations for the series CDn (n=24,25,..30) as a test for the convergence of the results from the PCA analysis, as well as treating problems with much higher dimensionality, e.g. CD100. | The LR-CDs, as the native CDs, are potential reagents for chiral resolution. With this application we can monitor the concerted motions of the atoms of the molecule in a few dimensions, making it easier to visualize and investigate these motions. Our efforts will be devoted to execute additional 50.0 ns simulations for the series CDn (n=24,25,..30) as a test for the convergence of the results from the PCA analysis, as well as treating problems with much higher dimensionality, e.g. CD100. | ||
== Scientific and Social Impact == | == Scientific and Social Impact == | ||
| + | |||
The results will provide invaluable guidelines for the conformational analysis of large rings that present interest as host systems in supramolecular functional architectures. | The results will provide invaluable guidelines for the conformational analysis of large rings that present interest as host systems in supramolecular functional architectures. | ||
The results of this work have potential useful applications for design of new materials and in new (nano) technologies, as well as in separation science (molecular recognition and separation of closely related compounds, including geometrical and structural isomers) and for the pharmaceutical industry (different pharmacological activity of enantiomers of a chiral compound). | The results of this work have potential useful applications for design of new materials and in new (nano) technologies, as well as in separation science (molecular recognition and separation of closely related compounds, including geometrical and structural isomers) and for the pharmaceutical industry (different pharmacological activity of enantiomers of a chiral compound). | ||
| - | == Collaborations | + | == Collaborations == |
| - | UAB-Barcelona | + | |
| + | * UAB-Barcelona | ||
| + | |||
| + | == Beneficiaries == | ||
| + | |||
| + | ''Tobefilledin'' | ||
| + | |||
| + | == Number of users == | ||
| + | |||
| + | ''Tobefilledin'' | ||
| + | |||
| + | == Development Plan == | ||
| + | |||
| + | * Concept: ''Tobefilledin'' | ||
| + | * Start of alpha stage: ''Tobefilledin'' | ||
| + | * Start of beta stage: ''Tobefilledin'' | ||
| + | * Start of testing stage: ''Tobefilledin'' | ||
| + | * Start of deployment stage: ''Tobefilledin'' | ||
| + | * Start of production stage: ''Tobefilledin'' | ||
| + | |||
| + | == Resource Requirements == | ||
| + | |||
| + | * Number of cores required for a single run: ''From Tobefilledin to 1000'' | ||
| + | * Minimum RAM/core required : ''1 GB'' | ||
| + | * Storage space during a single run : ''< 1TB'' | ||
| + | * Long-term data storage : ''< 500 GB'' | ||
| + | * Total core hours required: ''Tobefilledin'' | ||
== Technical features and HP-SEE implementation == | == Technical features and HP-SEE implementation == | ||
| + | |||
* Primary programming language : ''FORTRAN'' | * Primary programming language : ''FORTRAN'' | ||
* Parallel programming paradigm : ''MPI'' | * Parallel programming paradigm : ''MPI'' | ||
* Main parallel code : ''AMBER'' | * Main parallel code : ''AMBER'' | ||
* Pre/post processing code : ''Own development'' | * Pre/post processing code : ''Own development'' | ||
| - | * | + | * Application tools and libraries: ''Tobefilledin'' |
| - | + | ||
| - | + | ||
| - | + | ||
== Usage Example == | == Usage Example == | ||
| - | == | + | Tobefilledin |
| - | ''Tobefilledin'' | + | |
| + | == Infrastructure Usage == | ||
| + | |||
| + | * Home system: ''Tobefilledin'' | ||
| + | ** Applied for access on: ''Tobefilledin'' | ||
| + | ** Access granted on: ''Tobefilledin'' | ||
| + | ** Achieved scalability: ''Tobefilledin cores'' | ||
| + | * Accessed production systems: | ||
| + | # ''Tobefilledin'' | ||
| + | #* Applied for access on: ''Tobefilledin'' | ||
| + | #* Access granted on: ''Tobefilledin'' | ||
| + | #* Achieved scalability: ''Tobefilledin cores'' | ||
| + | #: | ||
| + | # ''Tobefilledin'' | ||
| + | #* Applied for access on: ''Tobefilledin'' | ||
| + | #* Access granted on: ''Tobefilledin'' | ||
| + | #* Achieved scalability: ''Tobefilledin cores'' | ||
| + | #: | ||
| + | * Porting activities: ''Tobefilledin'' | ||
| + | * Scalability studies: ''Tobefilledin'' | ||
| + | |||
| + | == Running on Several HP-SEE Centres == | ||
| + | |||
| + | * Benchmarking activities and results: ''Tobefilledin'' | ||
| + | * Other issues: ''Tobefilledin'' | ||
| + | |||
| + | == Achieved Results == | ||
| + | |||
| + | Tobefilledin | ||
| + | |||
| + | == Publications == | ||
| + | |||
| + | * Tobefilledin | ||
| + | * Tobefilledin | ||
| + | |||
| + | == Foreseen Activities == | ||
| + | * Tobefilledin | ||
| + | * Tobefilledin | ||
Revision as of 10:48, 23 January 2012
General Information
- Application's name: Principal component analysis of the conformational interconversions in large-ring cyclodextrins
- Application's acronym: PCACIC
- Virtual Research Community : Computational Chemistry Applications
- Scientific contact : Petko Ivanov, ivanov@bas.bg
- Technical contact : Petko Ivanov, ivanov@bas.bg
- Developers : Petko Ivanov, Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Lab. Physical Organic and Computational Chemistry
- Web site: Tobefilledin
Short Description
A new class of compounds, the large-ring cyclodextrins (LR-CDs), attracted attention in recent years, and advances were marked in the study of their physicochemical properties, in spite of existing difficulties in their synthesis, isolation and purification. Since CDs consist of optically active D-glucose units, they form a pair of diastereoisomeric complexes, usually of different stability, with a racemic compound. There is, however, limited information about either the structure of the macrocycles in solution, or their complex-forming properties.
In view of the difficulties in the purification of individual large-ring cyclodextrins, molecular dynamics simulation techniques provide a useful tool to gain insight into their conformational dynamics and the complex-forming ability. Using molecular dynamics simulations as a conformational search protocol, post-processing of the simulation trajectories is carried out by: (i) the MM/GBSA (Generalized Born/Surface Area (LCPO)) methodology in order to estimate energy data, and (ii) principal component analysis (PCA), also called quasiharmonic analysis or essential dynamics method.
These studies require enormous computational resources. It took only about five years in order to access an order of magnitude longer duration of the simulations for these systems. This is the reason why the use of HPC is necessary.
Previous releases of this application have been run on HPC resources of "Mare Nostrum" at the Barcelona Supercomputing Center.
Problems Solved
The LR-CDs, as the native CDs, are potential reagents for chiral resolution. With this application we can monitor the concerted motions of the atoms of the molecule in a few dimensions, making it easier to visualize and investigate these motions. Our efforts will be devoted to execute additional 50.0 ns simulations for the series CDn (n=24,25,..30) as a test for the convergence of the results from the PCA analysis, as well as treating problems with much higher dimensionality, e.g. CD100.
Scientific and Social Impact
The results will provide invaluable guidelines for the conformational analysis of large rings that present interest as host systems in supramolecular functional architectures.
The results of this work have potential useful applications for design of new materials and in new (nano) technologies, as well as in separation science (molecular recognition and separation of closely related compounds, including geometrical and structural isomers) and for the pharmaceutical industry (different pharmacological activity of enantiomers of a chiral compound).
Collaborations
- UAB-Barcelona
Beneficiaries
Tobefilledin
Number of users
Tobefilledin
Development Plan
- Concept: Tobefilledin
- Start of alpha stage: Tobefilledin
- Start of beta stage: Tobefilledin
- Start of testing stage: Tobefilledin
- Start of deployment stage: Tobefilledin
- Start of production stage: Tobefilledin
Resource Requirements
- Number of cores required for a single run: From Tobefilledin to 1000
- Minimum RAM/core required : 1 GB
- Storage space during a single run : < 1TB
- Long-term data storage : < 500 GB
- Total core hours required: Tobefilledin
Technical features and HP-SEE implementation
- Primary programming language : FORTRAN
- Parallel programming paradigm : MPI
- Main parallel code : AMBER
- Pre/post processing code : Own development
- Application tools and libraries: Tobefilledin
Usage Example
Tobefilledin
Infrastructure Usage
- Home system: Tobefilledin
- Applied for access on: Tobefilledin
- Access granted on: Tobefilledin
- Achieved scalability: Tobefilledin cores
- Accessed production systems:
- Tobefilledin
- Applied for access on: Tobefilledin
- Access granted on: Tobefilledin
- Achieved scalability: Tobefilledin cores
- Tobefilledin
- Applied for access on: Tobefilledin
- Access granted on: Tobefilledin
- Achieved scalability: Tobefilledin cores
- Porting activities: Tobefilledin
- Scalability studies: Tobefilledin
Running on Several HP-SEE Centres
- Benchmarking activities and results: Tobefilledin
- Other issues: Tobefilledin
Achieved Results
Tobefilledin
Publications
- Tobefilledin
- Tobefilledin
Foreseen Activities
- Tobefilledin
- Tobefilledin
