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
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
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
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
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
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
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
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
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
9 matches
Mail list logo