[gmx-users] About Free energy surface .....g_sas

2013-04-04 Thread rama david
Dear Friends, I simulated the 4 peptide in water box . As they come close to each other they start to from anti-parallel beta sheet structure. Now I want to draw the Free energy surface for the same ..How is there pot energy ??? Would you please tell me how to do it .. ( I read about

Re: [gmx-users] About Free energy surface .....g_sas

2013-04-04 Thread Justin Lemkul
On 4/4/13 2:14 AM, rama david wrote: Dear Friends, I simulated the 4 peptide in water box . As they come close to each other they start to from anti-parallel beta sheet structure. Now I want to draw the Free energy surface for the same ..How is there pot energy ??? Would you please

Re: [gmx-users] About Free energy surface .....g_sas

2013-04-04 Thread rama david
Thank you justin, I read the articles, archive and also g_sham -h, As I mentioned in previous mail, I simulated four random coil peptide , they started to form Beta sheet structure after 20 ns ..( simulation time 100ns ) My interest is how to draw the Free energy diagram for Potential energy

Re: [gmx-users] About Free energy surface .....g_sas

2013-04-04 Thread Justin Lemkul
On 4/4/13 5:50 AM, rama david wrote: Thank you justin, I read the articles, archive and also g_sham -h, As I mentioned in previous mail, I simulated four random coil peptide , they started to form Beta sheet structure after 20 ns ..( simulation time 100ns ) My interest is how to draw the

Re: [gmx-users] About Free energy surface .....g_sas

2013-04-04 Thread rama david
Thank you a lot justin for offering me help. I am interested to use g_sham ..( And if the other command give me my output, I am also interested to know the other way ) I was confuse with the input that I have to give with g_sham. I proceed the following command g_energy is used to get

Re: [gmx-users] About Free energy surface .....g_sas

2013-04-04 Thread Justin Lemkul
On 4/4/13 9:37 AM, rama david wrote: Thank you a lot justin for offering me help. I am interested to use g_sham ..( And if the other command give me my output, I am also interested to know the other way ) I was confuse with the input that I have to give with g_sham. I proceed the following

Re: [gmx-users] About Free energy surface .....g_sas

2013-04-04 Thread rama david
Dear Justin, Thank you a lot for help and kind passion to listen me. I finally come with the my desired out put. I I am grateful to you for help. With Best Wishes, Rama david On Thu, Apr 4, 2013 at 7:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/4/13 9:37 AM, rama david wrote: