AMBER md
@ambermdprog
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Amber is a suite of biomolecular simulation programs.
Joined January 2014
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Hi @LatinXChem, this is my work "Design and Application of Unnatural Base Pairs (UBPs) for Genetic Alphabet Expansion toward Semi-Synthetic Organism: A Classical MD approach" #LatinXChem22 #LXChemBio #BIO116 #MD #PolarizableForceField
@CisnerosRes
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So excited to be working with @awgoetz @darrinyork_lbsr and Metin Aktulga on this CSSI project! Amping up AMBER! @ambermdprog
https://t.co/3SWxhgcGuP
@NSF @MolSSI_NSF
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Our scientific commitee is made up by top Latin American researchers in their fields, all of them focused on the dissemination of science and scientific collaboration throughout the world
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I am honoured to have been elected as a member of the World Association of Theoretical and Computational Chemists (WATOC) Board. #WATOC2022
#ChemComp
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Nice to see our review on recent literature for QM in bio out. #compchem #quantum #machinelearning #drugdesign
Our mini-review on QM in the biological sciences is just out! https://t.co/PYhWEiQNJO
@MaduManathunga @awgoetz
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2022 Amber developers meeting. It was awesome to spend valuable time with these folks and see all the cool things coming into Amber soon. #CompChem @ambermdprog @ACSCOMP
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Amber-Developers meeting near Tampa, Florida! Last night sunset, this morning’s sunup, and developers still sleepy.
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prepareforleap: An automated tool for fast PDB-to-parameter generation https://t.co/KawP3Hnyuz
#CPPTRAJ #AMBERMD
onlinelibrary.wiley.com
The new “prepareforleap” command in the CPPTRAJ analysis software tool facilitates rapid PDB preparation for MD simulation via automation of the handling of disulfides, carbohydrate naming and...
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Our most recent paper with Dan Raleigh is out in JPC-B: interactions in protein denatured state probed via combination of expt and @ambermdprog alchemical free energy. https://t.co/bDb4OiUgqq
@jpcb_papers @SBUChemistry @LauferCenter
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The 2021 Amber developers meeting has begun! held virtually for the first time..
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Our new preprint with @RobCRizzo explores simulations of #SARSCoV2 spike RBD opening dynamics, pathways, free energy landscapes, mutations and virtual screening to probe a conserved hinge region. Thanks @AmaroLab for initial models! https://t.co/yh1gZEo1CN
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@daviddesancho If you wait for the Ampere cards, there is a new feature called MIG. You can partition your physical card into I think 8 virtual cards and run one MD in each partition assuming you have enough memory. As soon as we get our hands on one, we will try to test Amber and remd there
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Tired of the usual online cooking classes? Check out the new PLUMED Masterclass: a series of virtual and interactive lectures on @zoom_us focused on basic and advanced topics in #moleculardynamics #compchem #OpenSource. Places are limited! Register now: https://t.co/VIVOhfO7av
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- Interactive MD basis (engine: @openmm_toolkit; forcefield: @ambermdprog) works to keep interactions physically reasonable; - real-time validation of protein backbone and sidechain geometry; - continuously updated crystallographic maps. (4/17)
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