Re: [gmx-users] Need For a Script

2010-07-20 Thread Samrat Pal
? Samrat. From: Samrat Pal To: jalem...@vt.edu; Discussion list for GROMACS users Sent: Mon, July 19, 2010 10:00:27 AM Subject: Re: [gmx-users] Need For a Script Another thing is that I am not sure how to get the force-extension profile from the simulation

Re: [gmx-users] Need For a Script

2010-07-19 Thread Samrat Pal
advance Samrat Pal From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Fri, July 16, 2010 5:18:44 PM Subject: Re: [gmx-users] Need For a Script Samrat Pal wrote: > Dear All, > I am a new GROMACS user. I have been able to solvate a p

Re: [gmx-users] Need For a Script

2010-07-18 Thread ms
On 18/07/10 20:21, Samrat Pal wrote: I have been doing the pull simulations with your scripts and that are running fine. Thanks a lot. Can I use implicit solvent model in pulling simulations? I have gone through the mailing list and I found that it is not recommended (I may be wrong). Please sugg

Re: [gmx-users] Need For a Script

2010-07-18 Thread Samrat Pal
From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Fri, July 16, 2010 5:18:44 PM Subject: Re: [gmx-users] Need For a Script Samrat Pal wrote: > Dear All, > I am a new GROMACS user. I have been able to solvate a protein in a water

Re: [gmx-users] Need For a Script

2010-07-17 Thread Samrat Pal
Hey,.. Thank you for the script. I will keep in mind what you said next time. Samrat Pal From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Fri, July 16, 2010 5:18:44 PM Subject: Re: [gmx-users] Need For a Script Samrat Pal wrote: > D

Re: [gmx-users] Need For a Script

2010-07-16 Thread Justin A. Lemkul
Samrat Pal wrote: Dear All, I am a new GROMACS user. I have been able to solvate a protein in a water box and also to simulate it and unfold it by heating it. But I have facing problem with the script of AFM pulling. I want to unfold a protein by pulling the two ends of the protein. Can

[gmx-users] Need For a Script

2010-07-16 Thread Samrat Pal
Dear All, I am a new GROMACS user. I have been able to solvate a protein in a water box and also to simulate it and unfold it by heating it. But I have facing problem with the script of AFM pulling. I want to unfold a protein by pulling the two ends of the protein. Can anyone give me a full