[gmx-users] NPT not working

Hanin Omar hanin_omar85 at yahoo.com
Thu Nov 1 12:33:35 CET 2018

Dear all gromacs user;
I am new to gromacs, and i desperatly need help. I want to use gromacs to calculate the internal dynamics trajectory within a protein.
For my simulation i followed this protocol:
1)Use pdb2gmx to generate the gro file and topology ( i chose amber99SB and TIP3P water modrel)
2)Energy minimization in vacuum
3) set perodic boundery coditions
4)solvate the system
5) ADD ions to neutralize the system
6)Energy minimization of the solvated system
7) Position restrainted MD
8)Unrestraind MD ( NVT equiliberation)
9)Unrestraind MD ( NPT equiliberation)
10)Run MD simulation with the addition of RDC restraint in the topology like this
; Include Position restraint file
#ifdef POSRES
#include "RDC-restraint.itp"

The problem is i always get the following eroor when i run the last step
(Fatal error:
Error: Too many iterations in routine JACOBI)
I researched the error and some suggested that the system wasnt equiliberated enough, after checking it seems that the NPT part doesn't converge, i tried extending the time but that didnt solve it, i tired doing it in two steps: 1st NPT with thermostat = v - rescale and barostat = Berendsen for say 6.5 ps and then run 2ND NPT with thermostat = Nose-Hooover and barostat = Parinello -Rahman for 6.5 ps.But that also didnt help. can someone explain why is this happening( and if it has to do with the RDC constraints)? and how can i solve it?
THank you
Hanin Omar

Sent from my iPhone

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