<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt">I thank you all so much for aiding me on this matter, Jan, Peter and Justin. Now things are way clerarer!<br><br>Cheers,<br><br>Ricardo.<br><div><br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; margin-top: 5px; padding-left: 5px;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">De:</span></b> Peter C. Lai <pcl@uab.edu><br> <b><span style="font-weight: bold;">Para:</span></b> jalemkul@vt.edu; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Enviadas:</span></b> Sábado, 19 de Maio de 2012 1:01<br> <b><span
style="font-weight: bold;">Assunto:</span></b> Re: [gmx-users] Different Lipids into one Moleculetype (for position restrain)<br> </font> </div> <br>Thanks for the corrections. I had to mock up parts of it because usually<br>I only POSRE_RECEPTOR and POSRE_LIGAND. I also have a mix of putting the<br>position restraints in .itp file vs. in the topol.top, depending on how often<br>I am changing my topol.top (things like genion and g_membed modify them).<br><br><br>On 2012-05-18 11:00:55PM -0400, Justin A. Lemkul wrote:<br>> <br>> <br>> On 5/18/12 10:28 PM, Peter C. Lai wrote:<br>> > Synopsis: position restraints are coupled to the moleculetype. So you need to<br>> > define position restraints individually for each molecule type contiguous<br>> > with their topologies.<br>> ><br>> > There's a couple of ways to do it, using some simple #include and #define:<br>> ><br>> > You can restrain within each
molecule's own .itp file at the end, for example:<br>> ><br>> > popc.itp:<br>> > [ moleculetype ]<br>> > ; Name nrexcl<br>> > POPC 3<br>> ><br>> > [ atoms ]<br>> > ; nr type resnr residue atom cgnr charge mass typeB...<br>> > ; residue 1 POPC rtp POPC q 0.0<br>> > 1 NTL 1 POPC N 1 -0.6 14.007 ....<br>> > ...<br>> > 20 PL 1 POPC P 20 1.5 30.974 ....<br>> > ...<br>> ><br>> > [
dihedrals ]<br>> > ...<br>> > ; end of original file<br>> ><br>> > #ifdef POSRE_LIPID<br>> > [ position_restraints ]<br>> > ; atom type fx fy fz<br>> > 20 1 1000 1000 1000<br>> > ;restrain atom 20 in the molecule_type which is P<br>> > #endif<br>> ><br>> > Add something similar at the bottom of pope.itp.<br>> ><br>> > Then in your system-wide topol.top would look something like:<br>> ><br>> > #include "charmm36.ff/forcefield.itp" ;charmm36 lipids<br>> ><br>> > #include "popc.itp"<br>> > #include "pope.itp"<br>> ><br>> > #include "charmm36.ff/tips3p.itp" ;charmm waters<br>> ><br>> > [ system ]<br>> > POPC+POPE bilayer<br>> ><br>> > [ molecules ]<br>> > POPC 100<br>> > POPE
100<br>> > SOL 10000<br>> > ; or however many of each you have in your conf.gro file<br>> ><br>> > In your grompp.mdp, you'd have:<br>> ><br>> > #define -DPOSRE_LIPID ; to turn on position restraints in lipid .itps<br>> ><br>> > ------------------------------<br>> ><br>> > Another way to do it is to put the #ifdef POSRE_LIPID [ position_restraints ]<br>> > sections in the system-wide topol.top, but you'd need two of them, one per<br>> > lipid [ moleculetype ]:<br>> ><br>> > #include "charmm36.ff/forcefield.itp" ;charmm36 lipids<br>> ><br>> > #include "popc.itp"<br>> > #ifdef POSRE_LIPID<br>> > [ position_restraints ] ;for POPC<br>> > 20 1 1000 1000 1000<br>> > #endif<br>> ><br>> > #include "pope.itp"<br>> > #ifdef POSRE_LIPID<br>> > [ position_restraints
] ;for POPE<br>> > ...<br>> > #endif<br>> > ...<br>> ><br>> > The grompp.mdp file would continue to use #define -DPOSRE_LIPID to enable<br>> > those restraints.<br>> ><br>> > It is up to you how you want to modularize the restraints. You can even<br>> > use multiple #defines to restrain separately (although the resulting system<br>> > wouldn't necessarily be physically correct):<br>> ><br>> > As above topologies but:<br>> ><br>> > #ifdef -DPOSRE_POPC<br>> > ;position restraints for POPC<br>> > #endif<br>> ><br>> <br>> I think what you mean here is:<br>> <br>> #ifdef POSRE_POPC<br>> <br>> > #ifdef -DPOSRE_POPE<br>> > ;position restraints for POPE<br>> > #endif<br>> ><br>> <br>> and #ifdef POSRE_POPE.<br>> <br>> Otherwise, the define statement becomes very cumbersome (and perhaps faulty), with:<br>>
<br>> define = -D-DPOSRE_POPC -D-DPOSRE_POPE<br>> <br>> > and in grompp.mdp:<br>> ><br>> > #define -DPOSRE_POPC -DPOSRE_POPE<br>> > ;to restrain both<br>> ><br>> <br>> Note that for the .mdp, one does not use #define, but rather:<br>> <br>> define = -POSRE_POPC -DPOSRE_POPE<br>> <br>> -Justin<br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul, Ph.D.<br>> Research Scientist<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="mailto: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/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/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="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br>-- <br>==================================================================<br>Peter C. Lai | University of
Alabama-Birmingham<br>Programmer/Analyst | KAUL 752A<br>Genetics, Div. of Research | 705 South 20th Street<br><a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a> | Birmingham AL 35294-4461<br>(205) 690-0808 |<br>==================================================================<br><br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto: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/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post
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