Dear Justin<br><br>Thanks greatly for your suggestions. I will try a new series of EMs and NPT equilibrations to find whether it will be of effect.<br><br>Li<br><br><div class="gmail_quote">2011/5/14 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
li lv wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Justin<br>
<br>
<br>
Thanks for your reply. Generally I conduct the simulation following the tutorial on your website. The system contains an integrin alpha2b/beta3 transmembrane portion (PDB 2KNC) embedding in a 124-lipids DPPC bilayer and solvated in water. The initial membrane-protein system is built with INFLATEGRO. Here is the topology file of the system (not completed):<br>
<br>
“<br>
<br>
; Include forcefield parameters<br>
<br>
#include "ffG53a6_lipid.itp"<br>
<br>
<br>
; Include chain topologies<br>
<br>
#include "topol_A.itp"<br>
<br>
<br>
; Include Position restraint file<br>
<br>
#ifdef POSRES<br>
<br>
#include "posre_A.itp"<br>
<br>
#endif<br>
<br>
<br>
#include "topol_B.itp"<br>
<br>
<br>
; Include Position restraint file<br>
<br>
#ifdef POSRES<br>
<br>
#include "posre_B.itp"<br>
<br>
#endif<br>
<br>
<br>
; Include DPPC chain topology<br>
<br>
#include "dppc.itp"<br>
<br>
<br>
; Include water topology<br>
<br>
#include "spc.itp"<br>
<br>
<br>
#ifdef POSRES_WATER<br>
<br>
; Position restraint for each water oxygen<br>
<br>
[ position_restraints ]<br>
<br>
; i funct fcx fcy fcz<br>
<br>
1 1 1000 1000 1000<br>
<br>
#endif<br>
<br>
<br>
; Include generic topology for ions<br>
<br>
#include "ions.itp"<br>
<br>
<br>
[ system ]<br>
<br>
; Name<br>
<br>
Protein in water<br>
<br>
<br>
[ molecules ]<br>
<br>
; Compound #mols<br>
<br>
Protein_A 1<br>
<br>
Protein_B 1<br>
<br>
DPPC 124<br>
<br>
SOL 17185<br>
<br>
NA+ 2<br>
<br>
”<br>
<br>
<br>
For the details of energy minimization, here is one of the mdp files for energy minimization:<br>
<br>
“<br>
<br>
define = -DPOSRES<br>
<br>
integrator = cg<br>
<br>
emtol = 500.0 <br>
emstep = 0.01 <br>
nstcgsteep = 100<br>
<br>
nsteps = 50000 <br>
<br>
nstlist = 1 <br>
ns_type = grid<br>
<br>
rlist = 1.2 <br>
coulombtype = PME <br>
rcoulomb = 1.2 <br>
rvdw = 1.2 <br>
pbc = xyz<br>
<br>
<br>
<br>
freezegrps = Protein-H<br>
<br>
freezedim = Y Y Y <br>
”<br>
<br>
As you may notice, I froze the heavy atoms of the protein during the first energy minimization and then in the following the EMs the frozen group was MainChain, C-alpha and none in order. The system finally reached Fmax < 500.<br>
<br>
</blockquote>
<br></div></div>
But do you maintain position restraints? Restraints during minimization serve little use, and they actually are probably preventing some necessary structural changes from happening. I'd suspect that's the reason for your instability - you're not minimizing as well as your system requires.<br>
<br>
I would also say that there is no point in using both freezegrps and position restraints during equilibration, especially NPT, where freezegrps actually interfere with proper coordinate scaling. I would suggest you simply use position restraints.<div>
<div></div><div class="h5"><br>
<br>
-Justin<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]<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.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">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 www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">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>
</div></div></blockquote></div><br>