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Questions related from Souparno Adhikary
Hi, We have recently developed a system with Xeon E5-2699 v3 processors in two sockets and an RTX 2080 Super. We are running GROMACS 2020.2. The problem is, we are observing a serious decline in...
06 April 2021 8,420 3 View
We are investigating the temperature dependent anomalous activities of an enzyme and identified post translational modifications using tandem MS systems. Using unrestrained, nPT molecular dynamics...
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Hello, After reading the infamous publication "More Bang for your Bucks", I developed a workstation of my own using Xeon CPU (>3GHz, E5 series) along with one RTX and one GTX GPUs. In case of...
16 September 2019 1,948 7 View
Hi, I have a system which I am optimizing using B3LYP functional using 6-311++G basis set. The structure has 30Zn atoms. The number of basis sets is 1155. Number of atoms is 105. Gaussian...
01 December 2017 9,863 3 View
Can you suggest any way to calculate the average structure of a molecule from multiple frames in a PDB file. I want to do it in Python preferably. I have used Biopython and MDAnalysis before but I...
18 May 2017 9,475 4 View
I need to pre stain my protein samples before running sds page. Will mixing the coomassie brilliant blue help?
07 March 2015 4,403 9 View
1ns/hr for a 60k atom system unrestrained... GROMACS 2019... 1.0nm cutoff and 0.14 fft spacing... 160ns approx in 9 days... Count the power outage (totalling almost 9-10hrs last week), 3hrs rest...
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