RE: [gmx-users] afm simulation

2012-04-18 Thread Dallas Warren
- When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of swati patel Sent: Wednesday, 18 April 2012 8:12 PM To: Discussion list for GROMACS users Subject: [gmx-users] afm simulat

[gmx-users] afm simulation

2012-04-18 Thread swati patel
Hello everyone, I am trying to calculate the rupture force between streptavidin and biotin.Firstly,i have calculated the force by placing my complex in water.Now,i want to simulate my complex without placing it in water and then to calculate the rupture force.Can someone tell me,how to simulate a

Re: [gmx-users] afm simulation

2011-11-19 Thread Justin A. Lemkul
I attempted to send this before, but received an error message from the list. Let's try again... swati patel wrote: Hello Justin, I am following your tutorial on umbrella sampling.My project is on afm simulation of streptavidin-biotin complex.Till index.idx i ve created all my files.But as

[gmx-users] afm simulation

2011-11-19 Thread swati patel
Hello Justin, I am following your tutorial on umbrella sampling.My project is on afm simulation of streptavidin-biotin complex.Till index.idx i ve created all my files.But as per your tutorial you have discussed of frames extraction and configurations.Since i am dealing with pull afm,so do I also

Re: [gmx-users] afm simulation

2011-11-18 Thread Justin A. Lemkul
ibi2010...@iiita.ac.in wrote: Hello, I went through the tutorial umbrella sampling and i found that it is similar to afm simulation only using harmonic potential. May be i am wrong.Can you just satisfy my curiosity? They are functional equivalents. -Justin --

[gmx-users] afm simulation

2011-11-18 Thread ibi2010004
Hello, I went through the tutorial umbrella sampling and i found that it is similar to afm simulation only using harmonic potential. May be i am wrong.Can you just satisfy my curiosity? Thanx. - This email has been sent using ArithMail at "Indian Instit

[gmx-users] AFM Simulation

2011-06-13 Thread Michael McGovern
Hi everyone. I'm doing a simulation of a system where a peptide is linked to a surface and an AFM tip is brought in contact to do force measurements. The AFM tip moves very slowly (1nm/ms), so I'm simulating stationary tips at various distances. Does anyone know the most direct measurement f