Re: [gmx-users] gibbs free energy calculation

On 4/4/18 2:39 AM, Raag Saluja wrote: Hi! Thank you for your previous reply. You were right, my file was getting modified. I had not saved the page directly but had copy-pasted it in a textedit file. I am again stuck, though. I was trying to run job_0.sh and when I gave the command: gmx gromp

Re: [gmx-users] gibbs free energy calculation

Hi, That just means that that file doesn't exist, so something about your procedure is wrong. Find what files do exist, and where, and how that doesn't match the script. Mark On Wed, Apr 4, 2018 at 8:40 AM Raag Saluja wrote: > Hi! > > Thank you for your previous reply. You were right, my file

[gmx-users] gibbs free energy calculation

Hi! Thank you for your previous reply. You were right, my file was getting modified. I had not saved the page directly but had copy-pasted it in a textedit file. I am again stuck, though. I was trying to run job_0.sh and when I gave the command: gmx grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE

Re: [gmx-users] gibbs' free energy tutorial: help with write_mdp.pl

On 3/23/18 2:54 AM, Raag Saluja wrote: Hi! Thank you so much for your previous reply to my mail regarding Gibbs' free energy! However, I'm stuck again.. I tried the tutorial. On giving the command: perl write_mdp.pl em_steep.mdp I get these errors: Raags-MacBook-Pro:native tubulin gibbs P

[gmx-users] gibbs' free energy tutorial: help with write_mdp.pl

Hi! Thank you so much for your previous reply to my mail regarding Gibbs' free energy! However, I'm stuck again.. I tried the tutorial. On giving the command: perl write_mdp.pl em_steep.mdp I get these errors: Raags-MacBook-Pro:native tubulin gibbs Preetiwadhwa$ perl write_mdp.pl em_steep.mdp

[gmx-users] Gibbs free energy

Dear Prof. Spoel Thank you from your reply. Is good DoSPT code to obtain entropy for me?May I know your mean about pull out one lipid, Please? Best RegardsDina -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

Re: [gmx-users] Gibbs free energy

Den 2018-03-06 kl. 08:46, skrev dina dusti: Dear Gromacs users I have one question about obtaining of Gibbs free energy. I have one micellization system in NPT ensamble. Can I obtain the Gibbs free energy by G=H-TS? When H is obtained from g_energy and selection of enthalpy and S is obtained f

[gmx-users] Gibbs free energy

Dear Gromacs users I have one question about obtaining of Gibbs free energy. I have one micellization system in NPT ensamble. Can I obtain the Gibbs free energy by G=H-TS? When H is obtained from g_energy and selection of enthalpy and S is obtained from g_covar+g_anaeig.May I ask you to guide me

[gmx-users] Gibbs free energy

Dear Gromacs users I have one question about obtaining of Gibbs free energy. I have one micellization system in NPT ensamble. Can I obtain the Gibbs free energy by G=H-TS? When H is obtained from g_energy and selection of enthalpy and S is obtained from g_covar+g_anaeig.May I ask you to guide me

Re: [gmx-users] Gibbs' free energy in MD

You don't. Free energy calculations are much more involved than that, see http://www.alchemistry.org/wiki/Main_Page as a good resource for details. Plus, of course, there are heaps of journal articles on it and a good textbook will have details too. Catch ya, Dr. Dallas Warren Drug Delivery, Disp

[gmx-users] Gibbs' free energy in MD

Hi! How can I calculate Gibbs' free energy from the potential energy values obtained from the MD simulation? Regards, Raag -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gro

Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

Then, should I perform some more simulations at more different temperatures or should I go for simulated annealing? As of now, I actually have performed two simulations of each 100 ns at 300 and 310K only to differentiate two conditions. More elaborately speaking, I have modeled the outermembrane p

Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

On 22/09/15 07:42, Naba wrote: Thank you Justin. I have to deduce some inference from this figure. Please make me out about the following queries. On Mon, Sep 21, 2015 at 5:48 PM, Justin Lemkul wrote: On 9/21/15 4:00 AM, Naba wrote: Dear Gromacs users and Developers, I have performed dih

Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

Thank you Justin. I have to deduce some inference from this figure. Please make me out about the following queries. On Mon, Sep 21, 2015 at 5:48 PM, Justin Lemkul wrote: > > > On 9/21/15 4:00 AM, Naba wrote: > >> Dear Gromacs users and Developers, >> >> I have performed dihedral PCA for 4 extrac

Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

Sorry, I have posted my reply in wrong thread. On Tuesday, September 22, 2015, Padmani Sandhu wrote: > Hello justin, > > Thanks, actually I want to study movement of protons along the lenght of a > water channel. > > > Regards, > > > Padmani > > On Monday, September 21, 2015, Justin Lemkul > wr

Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

Hello justin, Thanks, actually I want to study movement of protons along the lenght of a water channel. Regards, Padmani On Monday, September 21, 2015, Justin Lemkul wrote: > [image: Boxbe] This message is eligible > for Automatic Cleanup! (jalem...@vt.edu >

Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

On 9/21/15 4:00 AM, Naba wrote: Dear Gromacs users and Developers, I have performed dihedral PCA for 4 extracellular loops of a transmembrane protein after successfully finishing 100 ns of simulation at 300 and 310 K. I obtained figures for each loops for two different temperatures as in this

[gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

Dear Gromacs users and Developers, I have performed dihedral PCA for 4 extracellular loops of a transmembrane protein after successfully finishing 100 ns of simulation at 300 and 310 K. I obtained figures for each loops for two different temperatures as in this link: http://s28.postimg.org/dlva5i4