[gmx-users] few doubts regarding 1-4 interaction

Ms. Aswathy S aswathys at amritapuri.amrita.edu
Tue Jun 30 16:03:13 CEST 2009

Hi gromacs users,

I am facing the same error during Production run that faced by so many gromacs users and I know this query has been answered for several times. But Could you please tell me some specific doubt regarding the 1-4 interaction error that usually occurs?

I have equilibrated my protein ligand system of around 600 ps and shown a satisfied level of equilibration. Then I moved to the Production run of 3ns. But shows the same 1-4 interaction error. My doubts are,

1. It was advised by gromacs experts that better I should go for another round of minimization. Is it on the equilibrated structure? 
2. If so Do i need to equilibrate again after minimization?
3. I have did 2500 steps of minimization on the structure which is equilibrated and then again run for 3ns production run But occured the same error at 3 lakh step?
 if I reduce my time step how that will affect this error(I have seen in the error section of gromacs that another possibility is to reduce the time step?)
Can you please tell me your suggestion on these??

Thank you.

Dept. Biotechnology
Ext. 3108

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