Yes, I overcome the last problems and I could see the pos.rest energy term in my log file. In order to create the itp files to include in top file, I opened the gro file which I entered as an input in my mdrun command. How might I check this issue that all the atoms in itp groups are involved in position restraints? Is there any solutions to check it?
Many many thanks for your replies Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Monday, March 18, 2013 4:46 PM Subject: Re: Fw: Fwd: [gmx-users] position restraints On 3/18/13 6:02 AM, Shima Arasteh wrote: > 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? > Were restraints correctly applied? Your last messages indicated fatal errors in trying to apply restraints - have you overcome those problems? Is there a position restraint energy term written to the .log and .edr files? Using such a huge force constant should not result in such RMSD values unless (1) they are not being applied or (2) whatever groups you have created for applying restraints do not cover all atoms that are being analyzed in the RMSD calculation, i.e. some are unrestrained and moving normally when you think they are being restrained. -Justin > > 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 -- 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
