hello everyone, pls tell me that whether we can use gromacs for simulating pdb with 3 or 4 residue. As i had done it with 4 residue with blocking group. But then i got the error for rvdw and rlist as they should be nearer to cutoff value. So instead of decreasing the value of rvdw. i increased my X, Y, Z coordinates. Tell me whether i m correct or not.
One more thing whether we can apply position restraint to all the atoms in the file.whether it will have any impact on my output. Silly Ouestion. But sorry for that. How we can come to know that to which atom i add position restraint in posre.itp file.Sorry i don't Know about this I read the manual but i m confused. Pls help me out Bhawana
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