With position restraints I got a new RMSD with the Min 0.05 and Max 0.11. I don't know if this range of deviation with position restraints is sensible or not! I can't believe with such a force of 100000 I still see deviations!
I'd prefer to get less deviation. Would it be possible by using a greater fc ? Is it sensible? Thanks for your suggestions in advance. Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Saturday, March 16, 2013 12:24 AM Subject: Re: Fw: Fwd: [gmx-users] position restraints On 3/15/13 8:50 AM, Shima Arasteh wrote: > Dear users, > > > Although I put the position restraints on backbone, I get RMSD around 0.2 nm. > Is it usual? No, 0.2 nm is very high. With position restraints, offhand I would think around 0.05 nm or less would be indicative of proper restraints. > This deviation is just for a minimization step only. I' m on doubt about > keeping the backbone in a fix secondary structure. > I' d prefer to restraint the backbone completely. Is it possible? > Yes, using genrestr to create a suitable posre.itp file that includes only backbone atoms. -Justin > Thanks in advance. > > > > Restraints allow, by definition, for slight deviations. > > Erik > * Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > > > > > Dear gmx users, > > I want to use restraints on backbone of my protein to keep its secondary > structure during minimization and equilibration steps. To do so, I > generated backbone-restrain.itp and then included it to top file. Next, > added define = -DPOSRES to minim.mdp file. > After minimization, when I check the minimization output file, I saw > that the backbone of input and output files are not exactly the same. > Is there any step which I have not done to set the restraints correctly? > > > Thanks in advance. > > Sincerely, > Shima > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist 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
