Hello, I am using gromacs 4.5.4. In g_energy I see an option about #surf*surfTen. Could you please clarify how it is calculated? In a system with a protein and water, what does it correspond to? Best,
Paymon -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: March-29-12 7:23 PM To: Acoot Brett; Discussion list for GROMACS users Subject: Re: [gmx-users] protein melting experiment by GROMACS Acoot Brett wrote: > Dear All, > > I remember before I have read a something on melting the protein from > a predefined starting temperature to a predefined end temperature by > MD, so that after the MD we can look at the whole process to see which > part of the protein unfold earlier, which part of the protein of the > protein unfold earlier. No I cannot find that introduction. > > After we equilibriate the protein system, will you please tell me how > to define the temperature gradient from the start temperature to the > end temperature in the mdp file? Or do you have a protocol on it? > See the manual regarding simulated annealing. -Justin -- ======================================== 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
