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P-LINCS specifications

Information


Unique identifier OMICS_24506
Name P-LINCS
Alternative names Parallel LINear Constraint Solver, LINCS

Maintainer


This tool is not maintained anymore.

Publications for Parallel LINear Constraint Solver

P-LINCS citations

 (377)
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Ion–ion interactions in the denatured state contribute to the stabilization of CutA1 proteins

2018
Sci Rep
PMCID: 5955972
PMID: 29769700
DOI: 10.1038/s41598-018-25825-7
call_split See protocol

[…] 1 ps. A Parrinello–Rahman barostat was used to maintain a pressure constant at 1.0 bar for 300 K and 6.0 bar for 400 K or 450 K with a relaxation time of 0.5 ps. Hydrogen atoms were constrained using LINCS, and MD simulations at 300 K, 400 K, and 450 K were conducted with an integration time step of 1 femtosecond (fs). Energy minimizations were done to remove bad van der Waals contacts. Next, the […]

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Structural basis of actin monomer re charging by cyclase associated protein

2018
Nat Commun
PMCID: 5951797
PMID: 29760438
DOI: 10.1038/s41467-018-04231-7
call_split See protocol

[…] eld for the proteins and the TIP3P model for water. The equations of motion were integrated using a leap-frog algorithm with a 2 fs time step. All bonds involving hydrogens were constrained using the LINCS algorithm. Long-range electrostatic interactions were treated by the smooth particle mesh Ewald scheme with a real-space cutoff of 1.2 nm, a Fourier spacing of 0.12 nm, and a fourth-order interp […]

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Identification and characterization of smallest pore forming protein in the cell wall of pathogenic Corynebacterium urealyticum DSM 7109

2018
BMC Biochem
PMCID: 5944148
PMID: 29743008
DOI: 10.1186/s12858-018-0093-9
call_split See protocol

[…] intained constant at 1 bar by using the Parrinello-Rahman barostat [] with semi-isotropic scaling with a coupling constant of 5 ps. Covalent bonds containing hydrogen atoms were constrained using the LINCS algorithm [] to be able to use an integration time step of 2 fs. Furthermore, two simulations of the octamer system were performed in the presence of an applied voltage of 100 mV to determine th […]

library_books

In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways

2018
Sci Rep
PMCID: 5932038
PMID: 29720700
DOI: 10.1038/s41598-018-25061-z

[…] step of 2 fs, with the only exception being the first equilibration run, in which a reduced time step of 1 fs was used for stability reasons. During the simulations, H-bonds were restrained using the LINCS algorithm, long range electrostatic interactions were treated using the Particle-Mesh Ewald (PME) method and van-der-Waals and Coulomb cutoffs were set to 1.2 nm. The TIP3P water model was used […]

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Self homodimerization of an actinoporin by disulfide bridging reveals implications for their structure and pore formation

2018
Sci Rep
PMCID: 5920107
PMID: 29700324
DOI: 10.1038/s41598-018-24688-2
call_split See protocol

[…] ino acids ionization was automatically adjusted to a neutral pH environment (pH = 7.0). Each MD system was subjected to a 100 ns simulation at 300 K using the isochoric isothermal (NVT) ensemble. The LINCS algorithm was used to constrain bond lengths and the integration time step was 2 fs. The long-range electrostatic interactions were treated until 1.2 nm using the particle-mesh Ewald method (PME […]

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Ginger (Zingiber officinale) phytochemicals—gingerenone A and shogaol inhibit SaHPPK: molecular docking, molecular dynamics simulations and in vitro approaches

2018
PMCID: 5879566
PMID: 29609660
DOI: 10.1186/s12941-018-0266-9
call_split See protocol

[…] rature of 300 K using Berendsen thermostat algorithm []. Following this, second equilibration was executed for 1 ns at constant pressure (NPT) of 1 bar maintained by Parrinello–Rahman barostat [] and LINCS [] was employed to constrain all bonds. Particle Mesh Ewald (PME) [] was used to calculate long-range electrostatic interactions with a cut-off of 1.2 nm. All short-range non-bonded interactions […]

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P-LINCS institution(s)
Max-Planck Institute for Polymer Research, Mainz, Germany

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