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Questions related from Souparno Adhikary
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...
09 September 2019 513 6 View
Hi, I am stuck in a weird situation. We want to observe some bond breaking-formation in a QM/MM simulation and for the rest of the project, for MD simulations, I have used GROMACS 2018 with 54a7...
02 February 2019 2,192 1 View
Hi, We were carrying out in vacuo energy minimization studies of a protein dimer (which is experimentally proven to be a dimer). Earlier, the same work has been done in our lab using an older...
05 May 2018 3,347 1 View
Hi, I am using MemBuilder II to build a mixed POPC:POPG membrane containing cholesterol. As you know, in MemBuilder, cholesterol is only supported for Gromos43a1. Previously, I did my simulation...
04 April 2018 1,683 0 View
I was trying to simulate a 512-DPPC membrane after developing it from Tieleman's model of 128-DPPC bilayer. I removed the initial periodicity and the water molecules using trjconv as suggested by...
03 March 2018 4,780 8 View
Can two forcefields (GROMOS53A6 for protein and CHARMM36 for lipid) be used for a protein-membrane simulation? It is absolutely necessary for me to use various kinds of membranes which mimic the...
03 March 2018 4,256 3 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...
12 December 2017 4,974 3 View
We are trying to join a dsRNA with a peptide using HyperChem. The moment we are trying to invoke the model builder, the double stranded structure just mashes up in a weird mesh like thing....
11 November 2017 3,318 2 View
All,We have several branched polymers (consisting of repeating units) of different levels of complexity. The branching increases exponentially with its so called "generation". We have drawn the...
09 September 2017 2,359 0 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...
05 May 2017 1,059 4 View
Hi, Below is my .mdp code for pulling as found in the tutorial by Justin Lemkul. I made the required changes to match my version syntax. pull = umbrellapull_ngroups = 2pull_group0 =...
03 March 2017 6,414 5 View
I was trying to extract the lines containing the informations about THR, TYR, PHE and TRP using C from a pdb file. It seems there are a lot of invisible ascii characters in the pdb file which...
02 February 2017 7,002 0 View
I need to pre stain my protein samples before running sds page. Will mixing the coomassie brilliant blue help?
03 March 2015 7,989 10 View
I just completed setting up my egpu setup for exediting GROMACS MD simulations. I have seen quite a few post here and there regarding this. So, I thought it would be a good idea to share my...
01 January 1970 1,391 5 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...
01 January 1970 538 6 View
