Re: [gmx-users] Gibbs free energy

I dont think it is a right place to ask this questions. It is not a tutor mailing list with basis of thermodynamics and statistical mechanics. Read before you use gmx. Steven On Tue, Dec 25, 2012 at 4:52 AM, mohammad agha mra...@yahoo.com wrote: Dear Steven, Many thanks from your help. In the

[gmx-users] Gibbs free energy

Dear GROMACS Users, I work with NPT ensemble. Is the total energy equal to Gibbs free energy? Thanks in advance. Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

Re: [gmx-users] Gibbs free energy

Obviosuly not. Total energy in MD = total potential energy + total kinetic energy. Read basis of MD. There are specific methods to get free energy which you should aslo read about. Steven On Mon, Dec 24, 2012 at 6:21 PM, mohammad agha mra...@yahoo.com wrote: Dear GROMACS Users, I work with

[gmx-users] Gibbs free energy

...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, December 25, 2012 2:26 AM Subject: Re: [gmx-users] Gibbs free energy Obviosuly not. Total energy in MD = total potential energy + total kinetic energy. Read basis of MD

[gmx-users] Gibbs free energy

Dear Steven, Many thanks from your help. In the manual at the section g_energy has been written that the gromacs calculate the delta G as is follows: Delta G = G(N,p,T) - G idgas(N,p,T) = kT ln eˆ(Upot/kT) But I don't understand why Upot? to calculate of delta S, I know that delta S =

Re: [gmx-users] Gibbs free energy of binding

Dear Justin If I do two MD simulations for a short time in the same conditions(of course separately for protein and drug) and calculate total energy of each one and sum them with each other as E1 as nonbonding free energy of system. then a MD simulation for Protein-drug system in the same

Re: [gmx-users] Gibbs free energy of binding

Hi Mohsen, The mean energy difference is only one component of the free energy difference. Before you go any further I'd suggest reading a good book on molecular simulations, like 'Understanding Molecular Simulations' by Frenkel and Smit. There's a good reason free energy calculations cover

Re: [gmx-users] Gibbs free energy of binding

Dear Gromacs users I want to calculate Gibbs free energy too,but about Protein-drug binding. Please guide more clearly,what texts I need to read for learning how can I do it? Besides,g-energy has an option for estimating free energy from trajectory file(-fee option) I thought if I had a

Re: [gmx-users] Gibbs free energy of binding

mohsen ramezanpour wrote: Dear Gromacs users I want to calculate Gibbs free energy too,but about Protein-drug binding. Please guide more clearly,what texts I need to read for learning how can I do it? Look into the literature and nearly any of the popular simulation textbooks.

Re: [gmx-users] Gibbs free energy of binding

Dear Justin You are right,But I searched in tools and I found g_sham It is very useful tool for estimating Gibbs free energy,Enthalepy , emtropy and ... I think I can use from that for my calculation of binding free energy(In the other words,del G free energy of system ) how do you think about

Re: [gmx-users] Gibbs free energy of binding

mohsen ramezanpour wrote: Dear Justin You are right,But I searched in tools and I found g_sham It is very useful tool for estimating Gibbs free energy,Enthalepy , emtropy and ... I think I can use from that for my calculation of binding free energy(In the other words,del G free energy of

[gmx-users] Gibbs free energy of binding

Hi gromacs users Can I use gromacs for obtaining Gibbs free energy of binding of protein and dna? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before

Re: [gmx-users] Gibbs free energy of binding

shahab shariati wrote: Hi gromacs users Can I use gromacs for obtaining Gibbs free energy of binding of protein and dna? Yes. I would suggest you read about potential of mean force calculations. -Justin -- Justin A. Lemkul Ph.D. Candidate

[gmx-users] Gibbs free energy of binding

Shahab, Justin is entirely correct, you should read about potential of mean force calculations, the gromacs pull code, and the gromacs free energy code. However, an important question is if you can *converge* the free energy of macromolecular binding. If you don't know the bound state,