Protein Simulation is giving too many LINCS errors and the program terminates in 14 ps. I am using parameters as in sample mdp files.
Namdeo sir, I am using the default values in all the three mdp files. only changing- nsteps = 50000 ; total 100 ps. (which originally is 5000 and 10ps) in pr.mdp and full.mdp.
Bhavani sir, i have read the documentation u suggested. dont know how to minimize the system
Dear Sweta,
here i have attached mdp files generally used in a protein in water simulation. Review the files use them and let me know required if any.
http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html
GO through tutorial it will helpful for you
Finally i solved the problem. the system was having nonzero total charge. i replaced some water with Cl ions to make the system neutral.
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