Respected Sir,<br><br>Greetings from Pawan.<br>I have used force constants of 100000 in position restraint .itp files for proteins as suggested in Dr. Tieleman' s webisite for Inflategro.<br>The mdp files are :<br><br>
<b>For energy minimization:</b><br>title = Protein in DPPC Bilayer<br>cpp = /usr/bin/cpp<br>define = -DPOSRES<br>integrator = steep<br>dt = 0.002<br>
nsteps = 50000<br><br>; Constrain control<br>constraints = none<br><br>; Output frequency for coords (x), velocities (v) and forces (f)<br>nstxout = 0<br>nstvout = 0<br>nstfout = 0<br>
nstxtcout = 0<br>nstenergy = 0<br><br>; nblist update frequency<br>nstlist = 10 <br><br>; ns algorithm <br>ns_type = grid<br>rlist = 1.8<br><br>; Method for doing VdW <br>
vdw-type = Cut-off<br>rvdw = 1.8<br><br>; Method for doing electrostatics <br>coulombtype = PME<br>rcoulomb = 1.8<br><br>; Center of mass control<br>nstcomm = 1<br>
<br>; Periodic boundary conditions <br>pbc = xyz<br><br>; Mode for center of mass motion removal<br>comm-mode = Linear<br><br>tcoupl = no<br>pcoupl = no<br>; Energy minimizing stuff<br>
emtol = 1000<br>emstep = 0.001<br><br><b>For position restraint mdrun:</b><br>title = Protein in DPPC Bilayer<br>cpp = /usr/bin/cpp<br>define = -DPOSRES<br>
constraints = all-bonds<br>constraint-algorithm= Lincs<br>integrator = md<br>dt = 0.002 <br>nsteps = 5000 <br>nstcomm = 1<br>nstxout = 50<br>
nstvout = 1000<br>nstfout = 0<br>nstlog = 10<br>nstenergy = 10<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>
rcoulomb = 1.0<br>vdw-type = Cut-off<br>rvdw = 1.0<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = berendsen<br>tc-grps = Protein DPPC<br>
tau_t = 0.1 0.1<br>ref_t = 300 300<br>; Energy monitoring<br>energygrps = Protein DPPC<br>;Pressure coupling is on<br>Pcoupl = berendsen<br>tau_p = 2.0 2.0<br>
compressibility = 4.5e-5 4.5e-5<br>ref_p = 1.0 1.0<br>Pcoupl_type = semiisotropic<br>; Generate velocites is on at 300 K.<br>gen_vel = no<br>gen_temp = 300.0<br>gen_seed = 173529<br>
<br><b>Topology file :</b><br>; Include forcefield parameters<br>#include "ffoplsaa.itp"<br>#include "lipid.itp"<br>#include "dppc.itp"<br><br>; Include chain topologies<br>#include "topol_A.itp"<br>
#include "topol_B.itp"<br>#include "topol_C.itp"<br><br>;#ifdef POSRES<br>;#include "lipid_posre.itp"<br>;#endif<br><br>; Include water topology<br>#ifdef FLEX_SPC<br>#include "flexspc.itp"<br>
#else<br>#include "spc.itp"<br>#endif<br><br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>
#endif<br><br>; Include generic topology for ions<br>#include "ions.itp"<br><br>[ system ]<br>; Name<br>PROTEIN IN DPPC BILAYER<br><br>[ molecules ]<br>; Compound #mols<br>Protein_A 1<br>Protein_B 1<br>
Protein_C 1<br>DPPC 926<br>;SOL 23552<br><br>Please help with some suggestions.<br><br>Thanking you,<br><br>Yours sincerely,<br>Pawan<br><br><div class="gmail_quote">On Mon, Mar 30, 2009 at 6:22 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<div> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Pawan Kumar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
Respected Sir,<br>
<br>
Greetings from Pawan.<br></div><div class="im">
I did the Inflategro procedure for the POPC bilayer generated using genconf.<br>
It took around 26 compressions for coming near the initial area (just above it).<br>
The minimization were all converged to Fmax < 1350.<br>
If I decrease the Fmax less than this I am getting machine precision.<br>
But when I proceeded with the final compressed structure for pr mdrun it gave lincs warnings and ended with segmentation fault.<br>
As an alternative to this bilayer I used the DPPC bilayer (pre-equilibrated) which is given in GMX-Benchmark distribution.<br>
I carried out the same steps of Inflategro. I used the cutoff of 14 A in the inflation and compression step also.<br>
In this case the the Steepest Descents converged to Fmax < 1000 in all the steps. The maximum force war never above 850.<br>
But when I did position restraint mdrun with the last compressed file I got Lincs warnings and Segementation fault after few steps (30 - 40 steps).<br>
Can you please help how to proceed ?<br>
<br>
</div></blockquote>
<br>
If the minimization procedure is adequately finishing, then the problem comes from something you are doing. If you post your .mdp file, we may be able to see if there are any obvious mistakes.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="h5">
Thanking you,<br>
<br>
Yours sincerely,<br>
Pawan<br>
<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<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>
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