RE: [gmx-users] Chemical Potential

...@gromacs.org] on behalf of Fabian Casteblanco [fabian.castebla...@gmail.com] Sent: Tuesday, May 22, 2012 11:54 PM To: gmx-users@gromacs.org Subject: [gmx-users] Chemical Potential Hello community, I'm just trying to explore what kind of calculations one can do on polymer systems (pure or in

[gmx-users] Chemical Potential

Hello community, I'm just trying to explore what kind of calculations one can do on polymer systems (pure or in water) in order to validate the force field works accurately for that system. I know there are basics such as density, volume, dH of vaporization, isothermal compressibility, heat capac

Re: [gmx-users] Chemical potential of protein

I want to calculate some thermodynamics property of the protein in vacuum - It can be chemical potential, free energy or surface tension. Just thinkin of something very simple. I want to use this property to coarse grain my protein and develope the force field for it. Would you suggest some easy th

Re: [gmx-users] Chemical potential of protein

Hi, Could you explain what you aim to do in more detail? 24 apr 2012 kl. 11.34 skrev Steven Neumann: > Dear Gmx users, > > Will standart Widom technique to calculate the chemical potential (e.g. for > water where we introduce extra water molecule and the interaction energy is > compared using

[gmx-users] Chemical potential of protein

Dear Gmx users, Will standart Widom technique to calculate the chemical potential (e.g. for water where we introduce extra water molecule and the interaction energy is compared using integrator: tpi) for the protein in vacuum? So in this case shall I introcuce extra protein and do it as with water

Re: [gmx-users] Chemical Potential

Thank you very much guys! I will search for some reading. If you can suggest a tutorial I will appreciate. On Thu, Jan 19, 2012 at 11:57 AM, René Pool wrote: > Hi, > > If I understand the question correctly, you want to know the water > chemical potential in the water/protein/ligand system. > If

Re: [gmx-users] Chemical Potential

Hi, If I understand the question correctly, you want to know the water chemical potential in the water/protein/ligand system. If so, in principle it should be possible to approximate the water chemical potential using test particle insertion. Gromacs has a utility for that. Cheers, René ===

Re: [gmx-users] Chemical Potential

On 2012-01-19 14:49, Ivan Gladich wrote: On 01/19/2012 11:34 AM, Steven Neumann wrote: Does anyone can help? Dear Gmx Users, I am wondering whether it is possible to obtain in Gromacs chemical potential e.g. of water in the protein - ligand system? Please, advise me to do some further reading, s

Re: [gmx-users] Chemical Potential

On 01/19/2012 11:34 AM, Steven Neumann wrote: Does anyone can help? Dear Gmx Users, I am wondering whether it is possible to obtain in Gromacs chemical potential e.g. of water in the protein - ligand system? Please, advise me to do some further reading, suggest method, maybe tutorial? Thank yo

[gmx-users] Chemical Potential

Does anyone can help? Dear Gmx Users, I am wondering whether it is possible to obtain in Gromacs chemical potential e.g. of water in the protein - ligand system? Please, advise me to do some further reading, suggest method, maybe tutorial? Thank you, Steven -- gmx-users mailing listgmx-

[gmx-users] Chemical Potential

Dear Gmx Users, I am wondering whether it is possible to obtain in Gromacs chemical potential e.g. of water in the protein - ligand system? Please, advise me to do some further reading, suggest method, maybe tutorial? Thank you, Steven -- gmx-users mailing listgmx-users@gromacs.org http://l

[gmx-users] Chemical potential

Dear Gmx Users, Can you please suggest a method (and further reading) for calculation of a chemical potential in Gromacs. Is it possible e.g. to calculate the chemical potential of my ligand or water in systerm consisting protein and ligand? Thank you Steven -- gmx-users mailing listgmx-use