Justin, Mark,<br><br>Ok<br>not I've included posre only to the lipid.itp wich consist of parameters for just 1 lipid<br><br>#ifdef POSRES_LIPID<br>#include "posre_lipid.itp"<br>#endif<br><br>to the minim.mdp I've included<br>
define = -DPOSRES_LIPID ; position restrain the lipids<br><br>As the result I have not obtained any error in grompp but after minimization my lipid bilayer was perturbed. I've used very strong posres. Why it have not worked ?<br>
<br><div class="gmail_quote">2011/10/31 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div></div><div class="h5"><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I've done all of that<br>
i have "posre_lipid.itp" - for 1 lipid ( posres for each of 50 atoms )<br>
<br>
<br>
I've included this in the topology of the bilayer<br>
<br>
; Include chain topologies<br>
#include "gromos53a6_lipid.ff/<u></u>forcefield.itp"<br>
#include "dppc.itp"<br>
<br>
; Include water topology<br>
#include "gromos53a6_lipid.ff/spc.itp"<br>
<br>
; Include ion topologies<br>
#include "gromos53a6_lipid.ff/ions.itp"<br>
<br>
#ifdef POSRES_LIPID<br>
#include "posre_lipid.itp"<br>
#endif<br>
<br>
; System specifications<br>
[ system ]<br>
128-Lipid DMPC Bilayer in water<br>
<br>
[ molecules ]<br>
; molecule name nr.<br>
DPPC 64<br>
SOL 1193<br>
SOL 690<br>
<br>
<br>
Also I've tried to make posre for whole system ( large posres ) but it also was finished with same error<br>
<br>
Fatal error:<br>
[ file posre_lipid.itp, line 6 ]:<br>
Atom index (2) in position_restraints out of bounds (1-1).<br>
This probably means that you have inserted topology section "position_restraints"<br>
in a part belonging to a different molecule than you intended to.<br>
In that case move the "position_restraints" section to the right molecule.<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/<u></u>Documentation/Errors</a><br>
<br>
What's most true for such multy system. Generate posre only for 1 part or for whole system?<br>
<br>
</blockquote>
<br></div></div>
Position restraints can only be applied on a [moleculetype] basis. Thus, order matters a lot, and the whole system cannot be restrained in one file. See the example here:<br>
<br>
<a href="http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds" target="_blank">http://www.gromacs.org/<u></u>Documentation/Errors#Atom_<u></u>index_n_in_position_<u></u>restraints_out_of_bounds</a><br>
<br>
As it stands now, the topology you've shown tries to apply lipid position restraints after the ions have been #included, which makes no sense at all.<div><div></div><div class="h5"><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
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</div></div></blockquote></div><br>