Re: [gmx-users] how to calculate kinetic constant?

2013-10-06 Thread rajat desikan
Hi Chris, The activation energy is obtained from the PMF well depth. So that leaves two variables k and A. If we get K at say 5 temepratures, and plot ln(k) vs. 1/T, the intercept will give us A. From that, at the temperature of interest, we can back out k. I will dig up the paper I saw this in. I

Re: [gmx-users] Regarding lipid bilayer simulation

2013-10-06 Thread Justin Lemkul
On 10/6/13 12:47 AM, hasthi wrote: Dear GROMACS users, I have been trying to simulate protein of my interest in lipid bilayer(POPC) . I am following the tutorial of KALP-15 in DPPC. When I try to minimise the system after generating system_inflated.gro. I get a

[gmx-users] change of bilayer structure during NVT equilibration

2013-10-06 Thread shahab shariati
Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER in a rectangular box. I did energy minimization successfully with following mdp file. -- ; Parameters describing what to do, when to stop and what

Re: [gmx-users] change of bilayer structure during NVT equilibration

2013-10-06 Thread Justin Lemkul
On 10/6/13 10:03 AM, shahab shariati wrote: Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER in a rectangular box. I did energy minimization successfully with following mdp file. -- ; Paramete

[gmx-users] pair distribution function

2013-10-06 Thread Archana Sonawani-Jagtap
I have simulations for different peptides in POPC bilayer. I want to calculate pair distribution function (pdf) between negatively charged phosphate residue of POPC and positively charged residues of peptide. Is there any tool available in gromacs for plotting these values? Secondly, how to calcu

Re: [gmx-users] pair distribution function

2013-10-06 Thread Justin Lemkul
On 10/6/13 10:36 AM, Archana Sonawani-Jagtap wrote: I have simulations for different peptides in POPC bilayer. I want to calculate pair distribution function (pdf) between negatively charged phosphate residue of POPC and positively charged residues of peptide. Is there any tool available in gr

Re: [gmx-users] pair distribution function

2013-10-06 Thread Archana Sonawani-Jagtap
Thank you. On Sun, Oct 6, 2013 at 8:12 PM, Justin Lemkul wrote: > > > On 10/6/13 10:36 AM, Archana Sonawani-Jagtap wrote: > >> I have simulations for different peptides in POPC bilayer. >> >> I want to calculate pair distribution function (pdf) between negatively >> charged phosphate residue of

[gmx-users] change of bilayer structure during NVT equilibration

2013-10-06 Thread shahab shariati
Dear Justin Very thanks for your quick reply. > Depends on how you prepared the system. For initial structure of system, I used coordination from website: http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html > Probably there were voids in the solvent or lipid headgroups that caused > distor

Re: [gmx-users] change of bilayer structure during NVT equilibration

2013-10-06 Thread Justin Lemkul
On 10/6/13 10:57 AM, shahab shariati wrote: Dear Justin Very thanks for your quick reply. Depends on how you prepared the system. For initial structure of system, I used coordination from website: http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html Note that these lipids require di