Bio-Analytical Mass Spectrometry
​Gabelica group
SERVERS
In our group we have high level know-how in multiscale molecular modelling methods.
With consolidated techniques based on computational results complemented by experimental measurements, we study the physical chemistry properties of nucleic acids in gas phase and solution, going from the single nucleobases up to high order structural motifs.
We perform quantum calculations to obtain physical properties (vibrational normal mode, electronic spectra) of nucleic acids using different levels of theory, such as Hartree-Fock, DFT and semi-empirical methods.
For the conformational sampling of molecules coupled with ion mobility experiments, we have developed several efficient protocols and strategies, through which we are able to atomistically resolve secondary, tertiary and quaternary folding of nucleic acids, both single and double stranded.
The protocols are based on unbiased and biased molecular dynamics (MD) techniques and on enhanced samplingmethods, such as replica exchange MD and simulated annealing.
Hardware:
Rack of blade-servers:
2 blade servers, 2 CPU Intel(R) Xeon(R) CPU E5-2650 0 @ 2.20GHz (16 cores, 32 threads)
3 blade servers, 2 CPU Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.40GHz (16 cores, 32 threads)
5 blade servers, 2 CPU Intel(R) Xeon(R) CPU E5-2660 v2 @ 2.60GHz (20 cores, 40 threads)
3 blade servers, 2CPU Intel Xeon silver, 256 GB RAM
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1 storage server of 50 TB
Old:
4 blade servers with 2 processors intel Xeon CPU E5-2000 (12 cores, 24 threads)
Software:
Amber1​2​, ​AmberTools20, ​​G​r​o​macs, ​NAMD, ​mopac, Gaussian16 B01, MOPAC, VMD, Chimera
