Aw: Re: [gmx-users] How to calculate enthalpy

2013-07-19 Thread lloyd riggs
through others first, and I do not know what you wished to do completly. Stephan Watkins Gesendet:Montag, 15. Juli 2013 um 19:25 Uhr Von:lloyd riggs lloyd.ri...@gmx.ch An:Discussion list for GROMACS users gmx-users@gromacs.org Betreff:Aw: Re: [gmx-users] How to calculate enthalpy Whats

[gmx-users] How to calculate enthalpy

2013-07-15 Thread pooja_gupta
Hi I want calculate the enthalpy of water molecule corresponding to protein folded and unfolded state. How much a single water molecule (enthalpy and free energy) contribute in folding ? Can we calculate enthapy from g_energy? -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] How to calculate enthalpy

2013-07-15 Thread Dr. Vitaly Chaban
Sure, you can. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 8:38 AM, pooja_gu...@nccs.res.in wrote: Hi I want calculate the enthalpy of water molecule corresponding to protein folded and unfolded state. How much a single water molecule (enthalpy and free energy) contribute in folding ?

Re: [gmx-users] How to calculate enthalpy

2013-07-15 Thread Albert
On 07/15/2013 10:20 AM, Dr. Vitaly Chaban wrote: Sure, you can. Dr. Vitaly V. Chaban I've got a question for it. Why the calculated entropy is negative? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

Re: [gmx-users] How to calculate enthalpy

2013-07-15 Thread pooja_gupta
Thanks Vitaly but how?? let's say the difference between unfolded to folded protein is 100 water molecules. What is the correct procedure to calculate (theoretically) the entrapy correspond to single water molecule for stabilizing/destabilizing the protein. help me Sure, you can. Dr.

Re: [gmx-users] How to calculate enthalpy

2013-07-15 Thread Dr. Vitaly Chaban
H = U +pV, all these terms are available through g_energy. Your resulting values will be per mole, so I would perform no additional normalization. Personally, I would simulate all cases (folded, unfolded, etc) with the same number of waters -- to avoid any possible artifacts. Dr. Vitaly V.

Aw: Re: [gmx-users] How to calculate enthalpy

2013-07-15 Thread lloyd riggs
enviornment where electrons are involved...means of coarse... Gesendet:Montag, 15. Juli 2013 um 10:34 Uhr Von:pooja_gu...@nccs.res.in An:vvcha...@gmail.com, Discussion list for GROMACS users gmx-users@gromacs.org Betreff:Re: [gmx-users] How to calculate enthalpy Thanks Vitaly but how?? lets say