<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hello Gaurav,<br>when i did g_rms with structre before energy minimisation as refrence and strucutre after energy minimisation, it came to be around 0.02.<br><br><div>--<br>Sonali Dhindwal</div><br><br>--- On <b>Thu, 20/5/10, Gaurav Goel <i><gauravgoeluta@gmail.com></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Gaurav Goel <gauravgoeluta@gmail.com><br>Subject: Re: [gmx-users] enegry minimisation<br>To: jalemkul@vt.edu, "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Thursday, 20 May, 2010, 5:36 PM<br><br><div class="plainMail">Can you try using g_rms to compare the difference between the<br>structures before and after EM.<br><br>-Gaurav<br><br>On Thu, May 20, 2010 at 7:53 AM, Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu"
href="/mc/compose?to=jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>><br>><br>> sonali dhindwal wrote:<br>>><br>>> Hello Gaurav,<br>>> Thanks for your reply,<br>>> I did position restrained enegry minimisation, and used following .mdp<br>>> file for the same<br>>><br>>> title = protein<br>>> cpp = /usr/bin/cpp ; the c pre-processor<br>>> define = -DPOSRE<br>>> constraints = none<br>>> integrator = steep<br>>> dt = 0.002 ; ps !<br>>> nsteps = 1000<br>>> nstlist = 10<br>>> ns_type = grid<br>>> rlist = 0.9<br>>> coulombtype = PME<br>>> rcoulomb = 0.9<br>>> rvdw = 0.9<br>>> fourierspacing = 0.12<br>>> fourier_nx = 0<br>>> fourier_ny = 0<br>>> fourier_nz
= 0<br>>> pme_order = 4<br>>> ewald_rtol = 1e-5<br>>> optimize_fft = yes<br>>> ;<br>>> ; Energy minimizing stuff<br>>> ;<br>>> emtol = 1000.0<br>>> emstep = 0.01<br>>> pbc = xyz<br>>><br>>> I included define = -DPOSRE, for restraining the atom postion,<br>>> I used posre.itp which was genertaed by pdb2gmx.<br>>><br>>> Have I done it correctly, because after this also many of the beeta sheets<br>>> have become short, forming loops.<br>><br>> Well, you haven't properly defined position restraints. The default<br>> (produced by pdb2gmx) requires "define = -DPOSRES" not "-DPOSRE." If you<br>> have for some reason modified the topology, then maybe your approach is<br>> correct, but otherwise your position restraints are not being applied.<br>><br>> I also find it very curious that
such substantial changes are taking place<br>> during a simple energy minimization. Are you sure the effects you are<br>> seeing are not simply due to the visualization software you are using<br>> guessing the incorrect secondary structure type? I have had that experience<br>> numerous times, especially in the case of beta-strands. DSSP tells me that,<br>> geometrically, I have beta-strands, but the visualization software renders<br>> coil structures.<br>><br>> In any case, large structural deviations during EM suggest something<br>> fundamentally wrong with the model. Usually the changes in EM are small,<br>> since it is performed at 0 K. Only huge forces would cause any sort of<br>> structural change.<br>><br>>> I also want to ask what is the meaning of fx fy and fz :<br>>><br>><br>> Force constants (kJ mol^-1 nm^-2) in the x, y, and z directions.<br>><br>>> ; atom type fx
fy fz<br>>> 1 1 1000 1000 1000<br>>> 5 1 1000 1000 1000<br>>> 6 1 1000 1000 1000<br>>> 7 1 1000 1000 1000<br>>> 8 1 1000 1000 1000<br>>> 9 1 1000 1000 1000<br>>> 11 1 1000 1000 1000<br>>> 12 1 1000 1000 1000<br>>> 15 1 1000 1000 1000<br>>> 18 1 1000 1000 1000<br>>> 19 1 1000 1000 1000<br>>> 20 1 1000 1000 1000<br>>> 21 1 1000 1000 1000<br>>> 22 1 1000 1000 1000<br>>> 23 1 1000 1000 1000<br>>><br>>> which is there in posre.itp file, and if these should have value of 1000<br>>> 1000 1000 each ?<br>>><br>><br>> These default values are typically quite sufficient to restrain the<br>> structure.<br>><br>> -Justin<br>><br>>> Thanks in advance.<br>>>
--<br>>> Sonali Dhindwal<br>>><br>>><br>>> --- On *Wed, 19/5/10, Gaurav Goel /<<a ymailto="mailto:gauravgoeluta@gmail.com" href="/mc/compose?to=gauravgoeluta@gmail.com">gauravgoeluta@gmail.com</a>>/* wrote:<br>>><br>>><br>>> From: Gaurav Goel <<a ymailto="mailto:gauravgoeluta@gmail.com" href="/mc/compose?to=gauravgoeluta@gmail.com">gauravgoeluta@gmail.com</a>><br>>> Subject: Re: [gmx-users] enegry minimisation<br>>> To: "sonali dhindwal" <<a ymailto="mailto:sonali11dhindwal@yahoo.co.in" href="/mc/compose?to=sonali11dhindwal@yahoo.co.in">sonali11dhindwal@yahoo.co.in</a>><br>>> Date: Wednesday, 19 May, 2010, 8:39 PM<br>>><br>>> For position restraints you need to do the following:<br>>><br>>> 1. define a name.itp file which looks like:<br>>><br>>> ; In this topology include file, you will find position
restraint<br>>> ; entries for all the heavy atoms in your original pdb file.<br>>> ; This means that all the protons which were added by pdb2gmx are<br>>> ; not restrained.<br>>><br>>> [ position_restraints ]<br>>> ; atom type fx fy fz<br>>> 1 1 1000 1000 1000<br>>> 5 1 1000 1000 1000<br>>> 6 1 1000 1000 1000<br>>> .......<br>>> .......<br>>> _____<br>>> 1,5,6 etc. are the atom indices you want to restrain. section 4.3.1<br>>> in manual.<br>>><br>>> 2. Add "define = -Dname" to your mdp file<br>>><br>>> 3. Add following lines to your topology file<br>>> ; Include Position restraint file<br>>> #ifdef name<br>>> #include "name.itp"<br>>> #endif<br>>><br>>> 4. compile and run.<br>>><br>>> I'm sure you will find mroe information on
position-restrain<br>>> simulation on gmx-users archive.<br>>><br>>> -Gaurav<br>>><br>>> On Wed, May 19, 2010 at 10:26 AM, sonali dhindwal<br>>> <<a ymailto="mailto:sonali11dhindwal@yahoo.co.in" href="/mc/compose?to=sonali11dhindwal@yahoo.co.in">sonali11dhindwal@yahoo.co.in</a><br>>> </mc/compose?to=<a ymailto="mailto:sonali11dhindwal@yahoo.co.in" href="/mc/compose?to=sonali11dhindwal@yahoo.co.in">sonali11dhindwal@yahoo.co.in</a>>> wrote:<br>>><br>>> Hello Gaurav,<br>>> Can you please help me in suggesting where should I look for<br>>> providing parameters to constrain the protein backbone and then<br>>> do EM and then how to run a short MD simulation by constraining<br>>> the protein backbone.<br>>> Sorry to bother you, but as I am new to Gromacs, your help will<br>>> be highly
appreciable.<br>>> Thanks in advance<br>>><br>>> --<br>>> Sonali Dhindwal<br>>><br>>><br>>> --- On *Wed, 19/5/10, Gaurav Goel /<<a ymailto="mailto:gauravgoeluta@gmail.com" href="/mc/compose?to=gauravgoeluta@gmail.com">gauravgoeluta@gmail.com</a><br>>> </mc/compose?to=<a ymailto="mailto:gauravgoeluta@gmail.com" href="/mc/compose?to=gauravgoeluta@gmail.com">gauravgoeluta@gmail.com</a>>>/* wrote:<br>>><br>>><br>>> From: Gaurav Goel <<a ymailto="mailto:gauravgoeluta@gmail.com" href="/mc/compose?to=gauravgoeluta@gmail.com">gauravgoeluta@gmail.com</a><br>>> </mc/compose?to=<a ymailto="mailto:gauravgoeluta@gmail.com" href="/mc/compose?to=gauravgoeluta@gmail.com">gauravgoeluta@gmail.com</a>>><br>>><br>>> Subject: Re: [gmx-users] enegry minimisation<br>>> To: "Discussion
list for GROMACS users"<br>>> <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a> </mc/compose?to=<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br>>> Date: Wednesday, 19 May, 2010, 6:44 PM<br>>><br>>><br>>> After adding water you can do energy minimization (EM) in<br>>> two steps:<br>>><br>>> 1. Constrain the protein backbone and do EM.<br>>> 2. Now do EM on the full system.<br>>> 3. Run a short MD simulation by constraining the protein<br>>> backbone.<br>>> The above three steps will help hydrate the protein molecule<br>>> with minimal distortion of protein structure.<br>>><br>>> 4. Now run a MD on full
system.<br>>><br>>> for details looks here:<br>>><br>>> <a href="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" target="_blank">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</a><br>>><br>>> <<a
href="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" target="_blank">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</a>><br>>><br>>> -Gaurav<br>>><br>>> On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal<br>>> <<a ymailto="mailto:sonali11dhindwal@yahoo.co.in" href="/mc/compose?to=sonali11dhindwal@yahoo.co.in">sonali11dhindwal@yahoo.co.in</a><br>>> <<a href="http://mc/compose?to=sonali11dhindwal@yahoo.co.in"
target="_blank">http://mc/compose?to=sonali11dhindwal@yahoo.co.in</a>>> wrote:<br>>><br>>> Sorry, but I couldnt get your question,<br>>> I have used this .mdp file for energy minimisation after<br>>> addition of water and using<br>>><br>>> GROMOS96 43a1 force field :<br>>><br>>><br>>> title = drg_trp<br>>> cpp = /lib/cpp ; location of cpp on SGI<br>>> define = -DFLEX_SPC ; Use Ferguson’s Flexible water<br>>> model [4]<br>>> constraints = none<br>>> integrator = steep<br>>> dt = 0.002 ; ps !<br>>> nsteps = 2000<br>>> nstlist = 10<br>>> ns_type = grid<br>>> rlist = 0.9<br>>> coulombtype = PME ;
Use particle-mesh ewald<br>>> rcoulomb = 0.9<br>>> rvdw = 1.0<br>>> fourierspacing = 0.12<br>>> fourier_nx = 0<br>>> fourier_ny = 0<br>>> fourier_nz = 0<br>>> pme_order = 4<br>>> ewald_rtol = 1e-5<br>>> optimize_fft = yes<br>>> ;<br>>> ; Energy minimizing stuff<br>>> ;<br>>> emtol = 1000.0<br>>> emstep = 0.01<br>>><br>>> I hope it will help you to guide me further<br>>> Thanks<br>>> --<br>>> Sonali Dhindwal<br>>><br>>><br>>> --- On *Wed, 19/5/10, Erik Marklund<br>>> /<<a ymailto="mailto:erikm@xray.bmc.uu.se"
href="/mc/compose?to=erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a><br>>> <<a href="http://mc/compose?to=erikm@xray.bmc.uu.se" target="_blank">http://mc/compose?to=erikm@xray.bmc.uu.se</a>>>/* wrote:<br>>><br>>><br>>> From: Erik Marklund <<a ymailto="mailto:erikm@xray.bmc.uu.se" href="/mc/compose?to=erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a><br>>> <<a href="http://mc/compose?to=erikm@xray.bmc.uu.se" target="_blank">http://mc/compose?to=erikm@xray.bmc.uu.se</a>>><br>>> Subject: Re: [gmx-users] enegry minimisation<br>>> To: "Discussion list for GROMACS users"<br>>> <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>> <<a href="http://mc/compose?to=gmx-users@gromacs.org"
target="_blank">http://mc/compose?to=gmx-users@gromacs.org</a>>><br>>> Date: Wednesday, 19 May, 2010, 5:31 PM<br>>><br>>><br>>> sonali dhindwal skrev:<br>>> > Hello All<br>>> > This question may sound trivial to many, but as i<br>>> am new to this field, please help.<br>>> > I want to ask a question regarding my previous<br>>> query of distortion of protein strucutre after<br>>> molecular dynamcs simulation.<br>>> > I have noticed that after enegry minimisation<br>>> using steepest decent algorithm, using emtol of 1000<br>>> kJ mol^-1 nm^-1 , large amount of distortion occurs.<br>>> > So is it necessary to do enegry
minimisation step<br>>> before MD, because this is my modeled protein, and i<br>>> have already done energy minimisation using<br>>> different program and after that I have done<br>>> refinement also.<br>>> > Thanks and regards<br>>> > ^<br>>> ><br>>> ><br>>> > --<br>>> > Sonali Dhindwal<br>>> ><br>>> ><br>>> So how has your system setup changed since your<br>>> previous EM? Addition of water? Cutoffs? PME?<br>>><br>>> -- -----------------------------------------------<br>>> Erik Marklund, PhD student<br>>>
Dept. of Cell and Molecular Biology, Uppsala<br>>> University.<br>>> Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>>> phone: +46 18 471 4537 fax: +46 18 511 755<br>>> <a ymailto="mailto:erikm@xray.bmc.uu.se" href="/mc/compose?to=erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a><br>>> <<a href="http://mc/compose?to=erikm@xray.bmc.uu.se" target="_blank">http://mc/compose?to=erikm@xray.bmc.uu.se</a>><br>>> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a><br>>><br>>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>> <<a href="http://mc/compose?to=gmx-users@gromacs.org"
target="_blank">http://mc/compose?to=gmx-users@gromacs.org</a>><br>>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>>> Please search the archive at<br>>> <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>>> Please don't post (un)subscribe requests to the<br>>> list. Use the www interface or send it to<br>>> <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>>> <<a href="http://mc/compose?to=gmx-users-request@gromacs.org" target="_blank">http://mc/compose?to=gmx-users-request@gromacs.org</a>>.<br>>> Can't post?
Read<br>>> <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>>><br>>><br>>><br>>> --<br>>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>> <<a href="http://mc/compose?to=gmx-users@gromacs.org" target="_blank">http://mc/compose?to=gmx-users@gromacs.org</a>><br>>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>>> Please search the archive at<br>>> <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>>> Please don't post (un)subscribe requests to the
list.<br>>> Use the<br>>> www interface or send it to<br>>> <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>>> <<a href="http://mc/compose?to=gmx-users-request@gromacs.org" target="_blank">http://mc/compose?to=gmx-users-request@gromacs.org</a>>.<br>>> Can't post? Read<br>>> <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>>><br>>><br>>><br>>> -----Inline Attachment Follows-----<br>>><br>>><br>>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>> <<a
href="http://mc/compose?to=gmx-users@gromacs.org" target="_blank">http://mc/compose?to=gmx-users@gromacs.org</a>><br>>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br>>> before posting!<br>>> Please don't post (un)subscribe requests to the list. Use the<br>>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>>> <<a href="http://mc/compose?to=gmx-users-request@gromacs.org" target="_blank">http://mc/compose?to=gmx-users-request@gromacs.org</a>>.<br>>> Can't post? Read <a
href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>>><br>>><br>>><br>>><br>><br>> --<br>> ========================================<br>><br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>><br>> ========================================<br>> --<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the www interface<br>> or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>><br>--<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a
href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div></blockquote></td></tr></table><br>