Another thing is that I am not sure how to get the force-extension profile from the simulation trajectory?
Thanks Samrat ________________________________ From: Samrat Pal <psamra...@yahoo.com> To: jalem...@vt.edu; Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Sun, July 18, 2010 12:21:04 PM Subject: Re: [gmx-users] Need For a Script 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 suggest. Thanks in advance Samrat Pal ________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> 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 >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 script for that so that >I >can standardise my protocol? Suggestion is urgent. http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling Also, as a bit of advice, don't use the word "urgent" when asking for free help. You're hoping someone else (who is busy) will find time to solve an issue for you. -Justin > Thanks in advance > Samrat Pal > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
