Can you try using g_rms to compare the difference between the structures before and after EM.
-Gaurav On Thu, May 20, 2010 at 7:53 AM, Justin A. Lemkul <[email protected]> wrote: > > > sonali dhindwal wrote: >> >> Hello Gaurav, >> Thanks for your reply, >> I did position restrained enegry minimisation, and used following .mdp >> file for the same >> >> title = protein >> cpp = /usr/bin/cpp ; the c pre-processor >> define = -DPOSRE >> constraints = none >> integrator = steep >> dt = 0.002 ; ps ! >> nsteps = 1000 >> nstlist = 10 >> ns_type = grid >> rlist = 0.9 >> coulombtype = PME >> rcoulomb = 0.9 >> rvdw = 0.9 >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 4 >> ewald_rtol = 1e-5 >> optimize_fft = yes >> ; >> ; Energy minimizing stuff >> ; >> emtol = 1000.0 >> emstep = 0.01 >> pbc = xyz >> >> I included define = -DPOSRE, for restraining the atom postion, >> I used posre.itp which was genertaed by pdb2gmx. >> >> Have I done it correctly, because after this also many of the beeta sheets >> have become short, forming loops. > > Well, you haven't properly defined position restraints. The default > (produced by pdb2gmx) requires "define = -DPOSRES" not "-DPOSRE." If you > have for some reason modified the topology, then maybe your approach is > correct, but otherwise your position restraints are not being applied. > > I also find it very curious that such substantial changes are taking place > during a simple energy minimization. Are you sure the effects you are > seeing are not simply due to the visualization software you are using > guessing the incorrect secondary structure type? I have had that experience > numerous times, especially in the case of beta-strands. DSSP tells me that, > geometrically, I have beta-strands, but the visualization software renders > coil structures. > > In any case, large structural deviations during EM suggest something > fundamentally wrong with the model. Usually the changes in EM are small, > since it is performed at 0 K. Only huge forces would cause any sort of > structural change. > >> I also want to ask what is the meaning of fx fy and fz : >> > > Force constants (kJ mol^-1 nm^-2) in the x, y, and z directions. > >> ; atom type fx fy fz >> 1 1 1000 1000 1000 >> 5 1 1000 1000 1000 >> 6 1 1000 1000 1000 >> 7 1 1000 1000 1000 >> 8 1 1000 1000 1000 >> 9 1 1000 1000 1000 >> 11 1 1000 1000 1000 >> 12 1 1000 1000 1000 >> 15 1 1000 1000 1000 >> 18 1 1000 1000 1000 >> 19 1 1000 1000 1000 >> 20 1 1000 1000 1000 >> 21 1 1000 1000 1000 >> 22 1 1000 1000 1000 >> 23 1 1000 1000 1000 >> >> which is there in posre.itp file, and if these should have value of 1000 >> 1000 1000 each ? >> > > These default values are typically quite sufficient to restrain the > structure. > > -Justin > >> Thanks in advance. >> -- >> Sonali Dhindwal >> >> >> --- On *Wed, 19/5/10, Gaurav Goel /<[email protected]>/* wrote: >> >> >> From: Gaurav Goel <[email protected]> >> Subject: Re: [gmx-users] enegry minimisation >> To: "sonali dhindwal" <[email protected]> >> Date: Wednesday, 19 May, 2010, 8:39 PM >> >> For position restraints you need to do the following: >> >> 1. define a name.itp file which looks like: >> >> ; In this topology include file, you will find position restraint >> ; entries for all the heavy atoms in your original pdb file. >> ; This means that all the protons which were added by pdb2gmx are >> ; not restrained. >> >> [ position_restraints ] >> ; atom type fx fy fz >> 1 1 1000 1000 1000 >> 5 1 1000 1000 1000 >> 6 1 1000 1000 1000 >> ....... >> ....... >> _____ >> 1,5,6 etc. are the atom indices you want to restrain. section 4.3.1 >> in manual. >> >> 2. Add "define = -Dname" to your mdp file >> >> 3. Add following lines to your topology file >> ; Include Position restraint file >> #ifdef name >> #include "name.itp" >> #endif >> >> 4. compile and run. >> >> I'm sure you will find mroe information on position-restrain >> simulation on gmx-users archive. >> >> -Gaurav >> >> On Wed, May 19, 2010 at 10:26 AM, sonali dhindwal >> <[email protected] >> </mc/[email protected]>> wrote: >> >> Hello Gaurav, >> Can you please help me in suggesting where should I look for >> providing parameters to constrain the protein backbone and then >> do EM and then how to run a short MD simulation by constraining >> the protein backbone. >> Sorry to bother you, but as I am new to Gromacs, your help will >> be highly appreciable. >> Thanks in advance >> >> -- >> Sonali Dhindwal >> >> >> --- On *Wed, 19/5/10, Gaurav Goel /<[email protected] >> </mc/[email protected]>>/* wrote: >> >> >> From: Gaurav Goel <[email protected] >> </mc/[email protected]>> >> >> Subject: Re: [gmx-users] enegry minimisation >> To: "Discussion list for GROMACS users" >> <[email protected] </mc/[email protected]>> >> Date: Wednesday, 19 May, 2010, 6:44 PM >> >> >> After adding water you can do energy minimization (EM) in >> two steps: >> >> 1. Constrain the protein backbone and do EM. >> 2. Now do EM on the full system. >> 3. Run a short MD simulation by constraining the protein >> backbone. >> The above three steps will help hydrate the protein molecule >> with minimal distortion of protein structure. >> >> 4. Now run a MD on full system. >> >> for details looks here: >> >> http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ >> >> <http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ> >> >> -Gaurav >> >> On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal >> <[email protected] >> <http://mc/[email protected]>> wrote: >> >> Sorry, but I couldnt get your question, >> I have used this .mdp file for energy minimisation after >> addition of water and using >> >> GROMOS96 43a1 force field : >> >> >> title = drg_trp >> cpp = /lib/cpp ; location of cpp on SGI >> define = -DFLEX_SPC ; Use Ferguson’s Flexible water >> model [4] >> constraints = none >> integrator = steep >> dt = 0.002 ; ps ! >> nsteps = 2000 >> nstlist = 10 >> ns_type = grid >> rlist = 0.9 >> coulombtype = PME ; Use particle-mesh ewald >> rcoulomb = 0.9 >> rvdw = 1.0 >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 4 >> ewald_rtol = 1e-5 >> optimize_fft = yes >> ; >> ; Energy minimizing stuff >> ; >> emtol = 1000.0 >> emstep = 0.01 >> >> I hope it will help you to guide me further >> Thanks >> -- >> Sonali Dhindwal >> >> >> --- On *Wed, 19/5/10, Erik Marklund >> /<[email protected] >> <http://mc/[email protected]>>/* wrote: >> >> >> From: Erik Marklund <[email protected] >> <http://mc/[email protected]>> >> Subject: Re: [gmx-users] enegry minimisation >> To: "Discussion list for GROMACS users" >> <[email protected] >> <http://mc/[email protected]>> >> Date: Wednesday, 19 May, 2010, 5:31 PM >> >> >> sonali dhindwal skrev: >> > Hello All >> > This question may sound trivial to many, but as i >> am new to this field, please help. >> > I want to ask a question regarding my previous >> query of distortion of protein strucutre after >> molecular dynamcs simulation. >> > I have noticed that after enegry minimisation >> using steepest decent algorithm, using emtol of 1000 >> kJ mol^-1 nm^-1 , large amount of distortion occurs. >> > So is it necessary to do enegry minimisation step >> before MD, because this is my modeled protein, and i >> have already done energy minimisation using >> different program and after that I have done >> refinement also. >> > Thanks and regards >> > ^ >> > >> > >> > -- >> > Sonali Dhindwal >> > >> > >> So how has your system setup changed since your >> previous EM? Addition of water? Cutoffs? PME? >> >> -- ----------------------------------------------- >> Erik Marklund, PhD student >> Dept. of Cell and Molecular Biology, Uppsala >> University. >> Husargatan 3, Box 596, 75124 Uppsala, Sweden >> phone: +46 18 471 4537 fax: +46 18 511 755 >> [email protected] >> <http://mc/[email protected]> >> http://folding.bmc.uu.se/ >> >> -- gmx-users mailing list [email protected] >> <http://mc/[email protected]> >> 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 >> [email protected] >> <http://mc/[email protected]>. >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> >> -- >> gmx-users mailing list [email protected] >> <http://mc/[email protected]> >> 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 >> [email protected] >> <http://mc/[email protected]>. >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> >> -----Inline Attachment Follows----- >> >> >> -- gmx-users mailing list [email protected] >> <http://mc/[email protected]> >> 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 [email protected] >> <http://mc/[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> > > -- > ======================================== > > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list [email protected] 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. 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