[gmx-users] Error energy minimization on protein with implicit water

Dear Gromacs users, I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps followed are- pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap

[gmx-users] Error energy minimization on protein with implicit water

Dear Gromacs users, I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps followed are- pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap

Re: [gmx-users] Error energy minimization on protein with implicit water

On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar wrote: > > Dear Gromacs users, > > I have a MD simulated protein and i take frame from this and remove water > and add water implicit in the interface and want to do energy minimization > but while doing the minimization i get errors. The steps follow

Re: [gmx-users] Error energy minimization on protein with implicit water

lina wrote: On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar wrote: Dear Gromacs users, I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps

Re: [gmx-users] Error energy minimization on protein with implicit water

By setting the emtol to 1.0, didnt work. Anyother way i could figure out. On Thu, Feb 9, 2012 at 6:32 PM, Justin A. Lemkul wrote: > > > lina wrote: > >> On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar >> wrote: >> >>> Dear Gromacs users, >>> >>> I have a MD simulated protein and i take frame fro