[gmx-users] Protein-MG-GDP (Protein-Ion-ligand) system simulation

[neeru sharma]

Dear Gromacs users,

I have to simulate a system consisting of Protein+MG+GDP where Protein is
in complex with MG and GDP. I generated the GDP parameters using
antechamber and then converted the topology,coordinate and parameter files
to the corresponding gromacs format.
Then, I tried to start with the simulation using AMBER ff03 forcefield. The
system ran well till energy minimization step, but at equilibration steps
it is showing lincs error at NVT equilibration step.

I used 2 coupling groups for my system with lincs constraint algorithm as
follows:
*tc-grps     = Protein_MG_GDP Water_and_ions *

I tried turning off lincs warning too, den NVT equilibration was done
finely but the system was blowing up during NPT equilibration. I tried with
3-4 steps of minimization also, but it didnt work (I have tried with lincs
warning off in NPT too). I have visualized the NVT output trajectory and
compared it with the initial structure too, and the trajectory was fine.


I am unable to figure out the reason for why the system is blowing up. I am
following the drug-ligand simulation tutorial but still can't figure out
the problem. Can anyone suggest any possible means to overcome this
situation?


If anyone has simulated any similar system with Protein-ion-ligand complex
or have faced similar problem, please share with what to do now to resolve
this issue or to simulation such a system?
Any help will be highly appreciated.

Thanks

-----
Neeru Sharma,
Pune (India)
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