Dear researcher
I did a molecular dynamic simulation of wt and mutant protein. Till 10 ns the structure is stable but after 10 ns the mutant diamer is dissociated. I also attached a movie of mutant protein.
I want the answer of these questions
1- Is this realistic condition.
2- Can we predict the diamer dissociation from MDS study.
3- Are this happen due to mutation in protein.
4- Are this is an error of parameters file
Please suggest me. I am new in molecular dynamics.
That's just a periodicity effect. The dimer is not actually dissociating. Re-image the trajectory with trjconv.
Thanks sir,
But i already converted the trajectory using trajconv command with -pbc mol -ur compact -center flag. But this showed same problem.
Multimeric systems require a bit more care; you can't rely on default options all the time. Moreover, your command does nothing to actually center the molecules.
A dimer that is "split" across PBC still has its geometric center at the center of the box, so centering has to either be performed on one unit of the dimer or on interfacial residues, both of which require a custom index group.
Thanks sir,
I solved my problem. You are the only one which is solution of all the problems of gromacs. Thankyou so much sir
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