Yes, I did (constraints=none).<br><br>These are my conclusions.<br><br>Since I could do CG without my position restraint,<br>My .top doesn't include any constraint. (if my posre.itp is not constraint).<br>The manual says "SD is enough for general purpose".
<br>If one wants to do energy minimization with position restraint, then do SD only.<br><br>Thank you anyway.<br><br><br><div class="gmail_quote">On Jan 14, 2008 5:21 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">
jalemkul@vt.edu</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>Perhaps this is too obvious to be the solution, but have you considered setting
<br>'constraints = none' in your em.mdp file? After all, as Mark originally<br>pointed out, the documentation will tell you that constraints and CG don't mix.<br><br>-Justin<br><div><div></div><div class="Wj3C7c">
<br>Quoting Myunggi Yi <<a href="mailto:myunggi@gmail.com">myunggi@gmail.com</a>>:<br><br>> Sorry this is my top file.<br>><br>> #include "ffgmx.itp"<br>> #include "../lipid.popc.itp"
<br>> #include "popc.itp"<br>> #include "pro.itp"<br>> #include "ions.itp"<br>> #include "spc.itp"<br>><br>> Which one defines constraints?<br>><br>><br>> On Jan 14, 2008 4:35 PM, Myunggi Yi <
<a href="mailto:myunggi@gmail.com">myunggi@gmail.com</a>> wrote:<br>><br>> > Thnak you.<br>> ><br>> > I don't use any constrant like lincs or shake.<br>> > Why do I get the error message.
<br>> ><br>> ><br>> ><br>> > On Jan 14, 2008 4:11 PM, Mark Abraham < <a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br>> ><br>> > > Myunggi Yi wrote:
<br>> > > > Dear users,<br>> > > ><br>> > > > I'd like to restraint the protein during the minimization.<br>> > > > I've got the following message.<br>> > >
<br>> > > In GROMACS, restraints are different from constraints. Check out the<br>> > > manual for details.<br>> > ><br>> > > > ERROR: can not do Conjugate Gradients with constraints
<br>> > ><br>> > > Your .top is defining some constraints, and if you'd checked out the<br>> > > manual, you'd have confirmed that GROMACS can't handle constraints with<br>> > > the CG algorithm.
<br>> > ><br>> > > > em.mdp file<br>> > > > +++++++++++++++++++++<br>> > > > cpp = cpp<br>> > > > include =<br>> > > > define = -DPOSRES
<br>> > > > define = -DFLEXIBLE<br>> > > ><br>> > > > ; RUN CONTROL PARAMETERS<br>> > > > integrator = cg<br>> > > > ; Start time and timestep in ps
<br>> > > > tinit = 0<br>> > > > dt = 0.001<br>> > > > nsteps = 250<br>> > > > +++++++++++++++++++++<br>> > > >
<br>> > > > How can I do this?<br>> > ><br>> > > Either don't use constraints or don't use CG.<br>> > ><br>> > > Mark<br>> > > _______________________________________________
<br>> > > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> > > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.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<br>> > > posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the
<br>> > > www interface or send it to <a href="mailto: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>> ><br>> ><br>> > --<br>> > Best wishes,<br>> ><br>> > MYUNGGI YI<br>> > ==================================
<br>> > KLB 419<br>> > Institute of Molecular Biophysics<br>> > Florida State University<br>> > Tallahassee, FL 32306<br>> ><br>> > Office: (850) 645-1334<br></div></div>> > <a href="http://www.scs.fsu.edu/%7Emyunggi" target="_blank">
http://www.scs.fsu.edu/~myunggi</a> <<a href="http://www.scs.fsu.edu/%7Emyunggi" target="_blank">http://www.scs.fsu.edu/%7Emyunggi</a>><br>> ><br>><br>><br>><br>> --<br><div class="Ih2E3d">> Best wishes,
<br>><br>> MYUNGGI YI<br>> ==================================<br>> KLB 419<br>> Institute of Molecular Biophysics<br>> Florida State University<br>> Tallahassee, FL 32306<br>><br>> Office: (850) 645-1334
<br>> <a href="http://www.scs.fsu.edu/%7Emyunggi" target="_blank">http://www.scs.fsu.edu/~myunggi</a><br>><br><br><br><br></div>========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant
<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br><a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (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><div><div></div><div class="Wj3C7c">_______________________________________________<br>gmx-users mailing list
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.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 href="mailto: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></div></blockquote></div><br>
<br clear="all"><br>-- <br>Best wishes,<br><br>MYUNGGI YI<br>==================================<br>KLB 419<br>Institute of Molecular Biophysics<br>Florida State University<br>Tallahassee, FL 32306<br><br>Office: (850) 645-1334
<br><a href="http://www.scs.fsu.edu/~myunggi">http://www.scs.fsu.edu/~myunggi</a>