Dear Gromacs Users!<br><br><br>At the present time I'm simulating small peptide (11 a.c in coiled conformation) in water.<br><br>I've desided to use parameters from Lysozyme simmulation ( opls ff for parametrisation and all mdp parameters from that simulation).<br>
<br>Because my peptide was smaller than typical globular protein I've desided to use bigger periodical box than in tutorial<br><br>I've used editconf -c -d 1.5 -bt cubic instead of 1.0 nm in tutorial wich resulted in bigger box relative peptide size.<br>
<br>so i have this box vectors 5.39318 5.39318 5.39318<br><br>My experiment was in full agreement with the above tutorial until NVP phase was conducted. I have conducted 100ps equilibration but When I've checked average pressure it was 0.75 atm instead of 1 BAR and have big RMSD- 200. (also I've checked my system visually but it looks fine- I have not pointed any artifacts linked with unstable pressure like voids in the solvent etc). Should I equilibrate my sustem longer until pressure would not be stabilized to reference BAR? What another options should i take into account during simulation of the small peptides ?<br>
<br>Thanks,<br><br>James<br>