Re: [gmx-users] calculation of self energy of protein

2017-03-27 Thread Justin Lemkul
On 3/27/17 2:02 AM, Saumyak Mukherjee wrote: Dear Justin, Is there any way to get just the interaction energy between protein and water? In this case, the energy should not contain the self or inherent energy. Set the protein and water as separate energygrps and extract the relevant nonbon

Re: [gmx-users] calculation of self energy of protein

2017-03-26 Thread Saumyak Mukherjee
Dear Justin, Is there any way to get just the interaction energy between protein and water? In this case, the energy should not contain the self or inherent energy. Thanks & regards, Saumyak On 27 March 2017 at 11:27, Saumyak Mukherjee wrote: > Thank you very much. > > On 27 March 2017 at 02:2

Re: [gmx-users] calculation of self energy of protein

2017-03-26 Thread Saumyak Mukherjee
Thank you very much. On 27 March 2017 at 02:22, Justin Lemkul wrote: > > > On 3/26/17 4:49 PM, Saumyak Mukherjee wrote: > >> Dear Justin, >> >> Thanks for the reply. >> >> I have tried that already. I stripped out the protein trajectory using >> trjconv, created an appropriate .tpr file using tp

Re: [gmx-users] calculation of self energy of protein

2017-03-26 Thread Justin Lemkul
On 3/26/17 4:49 PM, Saumyak Mukherjee wrote: Dear Justin, Thanks for the reply. I have tried that already. I stripped out the protein trajectory using trjconv, created an appropriate .tpr file using tpbconv (I am using GROMACS 4.5.6), and recalculated energy using mdrun -rerun. But does the

Re: [gmx-users] calculation of self energy of protein

2017-03-26 Thread Saumyak Mukherjee
Dear Justin, Thanks for the reply. I have tried that already. I stripped out the protein trajectory using trjconv, created an appropriate .tpr file using tpbconv (I am using GROMACS 4.5.6), and recalculated energy using mdrun -rerun. But does the resulting .edr file include only the inherent ene

Re: [gmx-users] calculation of self energy of protein

2017-03-26 Thread Justin Lemkul
On 3/26/17 10:06 AM, Saumyak Mukherjee wrote: Yes, I need to calculate the inherent potential energy of the protein. You can strip the protein coordinates from the original trajectory, create a matching .tpr with convert-tpr and re-calculate energies with mdrun -rerun. The quantity is a f

Re: [gmx-users] calculation of self energy of protein

2017-03-26 Thread Saumyak Mukherjee
Yes, I need to calculate the inherent potential energy of the protein. On 26 March 2017 at 14:33, Souparno Adhikary wrote: > Do you mean the potential energy of the protein? > > On 26 Mar 2017 14:24, "Saumyak Mukherjee" > wrote: > > > Dear Users, > > > > How can the self energy of a protein be

Re: [gmx-users] calculation of self energy of protein

2017-03-26 Thread Souparno Adhikary
Do you mean the potential energy of the protein? On 26 Mar 2017 14:24, "Saumyak Mukherjee" wrote: > Dear Users, > > How can the self energy of a protein be calculated from GROMACS. This means > that I want only the inherent energy of the protein, excluding the > interaction energy with the surro

[gmx-users] calculation of self energy of protein

2017-03-26 Thread Saumyak Mukherjee
Dear Users, How can the self energy of a protein be calculated from GROMACS. This means that I want only the inherent energy of the protein, excluding the interaction energy with the surrounding solvent. Adding to this, is it possible to calculate such inherent energy of any selected domain in th