An enhanced version of SMMP—open-source software package for simulation of proteins

Eisenmenger, Frank; Hansmann, Ulrich H. E.; Hayryan, Shura; Hu, Chin Kun

doi:10.1016/j.cpc.2005.10.013

Cited by 48 publications

(35 citation statements)

References 15 publications

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“…Our simulations utilize the ECEPP/3 force field [10] as implemented in the 2005 version of the program package SMMP [11,12]. Here the interactions between the atoms within the homopolymer chain are approximated by a sum E ECEP P/3 consisting of electrostatic energy E C , a Lennard-Jones term E LJ , hydrogen-bonding term E HB and a torsion energy E T or :…”

Section: Methodsmentioning

confidence: 99%

On the helix-coil transition in alanine based polypeptides in gas phase

Wei

Nadler

Hansmann

2007

The Journal of Chemical Physics

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Using multicanonical simulations, we study the effect of charged end groups on helix formation in alanine based polypeptides. We confirm earlier reports that neutral poly-alanine exhibits a pronounced helix-coil transitions in gas phase simulations. Introducing a charged Lys + at the C-terminal stabilizes the α helix and leads to a higher transition temperature. On the other hand, adding the Lys + at the N-terminal inhibits helix formation. Instead, a more globular structure was found. These results are in agreement with recent experiments on alanine based polypeptides in gas phase. They indicate that present force fields describe accurately the intramolecular interactions in proteins.

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Section: Methodsmentioning

confidence: 99%

On the helix-coil transition in alanine based polypeptides in gas phase

Wei

Nadler

Hansmann

2007

The Journal of Chemical Physics

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“…Our investigations rely on simulations of Glu 10 with the ECEPP/3 force field 10 as implemented in the 2005 version of the program package SMMP 11,12 . Here the interactions between the atoms within the homopolymer chain are approximated by a sum E ECEP P/3 consisting of electrostatic energy E C , a Lennard-Jones term E LJ , hydrogen-bonding term E hb and a torsion energy E tor :…”

Section: Methodsmentioning

confidence: 99%

Side-chain and backbone ordering in a polypeptide

Wei

Nadler

Hansmann

2006

The Journal of Chemical Physics

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We report results from multicanonical simulations of polyglutamic acid chains of length ten residues. For this simple polypeptide we observe a decoupling of backbone and side-chain ordering in the folding process. While the details of the two transitions vary between the peptide in gas phase and in an implicit solvent, our results indicate that, independent of the specific surroundings, upon continuously lowering the temperature side-chain ordering occurs only after the backbone topology is completely formed.

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“…Later, we compare Mont-Blanc against MareNostrum supercomputer on a subset of the applications to make a direct comparing between the two, in terms of performance and energy consumption. [14], [15] Electronic Structure BQCD [16] Quantum Chromodynamics MP2C Multi-Particle Collision Dynamics QuantumESPRESSO [17] Electronic Structure and Materials Modeling SMMP [18], [19], [20] Molecular Thermodynamics Alya [21], [22] Biomedical Mechanics COMD [23] Proxy for Molecular Dynamics LULESH [24], [25] Proxy for Hydrodynamics miniFE [26] Proxy for Finite Element Method…”

Section: Overall System Evaluationmentioning

confidence: 99%

The Mont-Blanc Prototype: An Alternative Approach for HPC Systems

Rajovic¹,

Rico

Mantovani

et al. 2016

SC16: International Conference for High Performance Computing, Networking, Storage and Analysis

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Abstract-High-performance computing (HPC) is recognized as one of the pillars for further advance of science, industry, medicine, and education. Current HPC systems are being developed to overcome emerging challenges in order to reach Exascale level of performance, which is expected by the year 2020. The much larger embedded and mobile market allows for rapid development of IP blocks, and provides more flexibility in designing an application-specific SoC, un turn giving possibility in balancing performance, energy-efficiency and cost. In the Mont-Blanc project, we advocate for HPC systems be built from such commodity IP blocks, currently used in embedded and mobile SoCs.As a first demonstrator of such approach, we present the MontBlanc prototype; the first HPC system built with commodity SoCs, memories, and NICs from the embedded and mobile domain, and offthe-shelf HPC networking, storage, cooling and integration solutions. We present the system's architecture, and evaluation including both performance and energy efficiency. Further, we compare the system's abilities against a production level supercomputer. At the end, we discuss parallel scalability, and estimate the maximum scalability point of this approach across a set of applications.

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An enhanced version of SMMP—open-source software package for simulation of proteins

Cited by 48 publications

References 15 publications

On the helix-coil transition in alanine based polypeptides in gas phase

On the helix-coil transition in alanine based polypeptides in gas phase

Side-chain and backbone ordering in a polypeptide

The Mont-Blanc Prototype: An Alternative Approach for HPC Systems

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