Respected Sir, Greetings from Pawan. I have used force constants of 100000 in position restraint .itp files for proteins as suggested in Dr. Tieleman' s webisite for Inflategro. The mdp files are :
*For energy minimization:* title = Protein in DPPC Bilayer cpp = /usr/bin/cpp define = -DPOSRES integrator = steep dt = 0.002 nsteps = 50000 ; Constrain control constraints = none ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 nstxtcout = 0 nstenergy = 0 ; nblist update frequency nstlist = 10 ; ns algorithm ns_type = grid rlist = 1.8 ; Method for doing VdW vdw-type = Cut-off rvdw = 1.8 ; Method for doing electrostatics coulombtype = PME rcoulomb = 1.8 ; Center of mass control nstcomm = 1 ; Periodic boundary conditions pbc = xyz ; Mode for center of mass motion removal comm-mode = Linear tcoupl = no pcoupl = no ; Energy minimizing stuff emtol = 1000 emstep = 0.001 *For position restraint mdrun:* title = Protein in DPPC Bilayer cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds constraint-algorithm= Lincs integrator = md dt = 0.002 nsteps = 5000 nstcomm = 1 nstxout = 50 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdw-type = Cut-off rvdw = 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein DPPC tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein DPPC ;Pressure coupling is on Pcoupl = berendsen tau_p = 2.0 2.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 Pcoupl_type = semiisotropic ; Generate velocites is on at 300 K. gen_vel = no gen_temp = 300.0 gen_seed = 173529 *Topology file :* ; Include forcefield parameters #include "ffoplsaa.itp" #include "lipid.itp" #include "dppc.itp" ; Include chain topologies #include "topol_A.itp" #include "topol_B.itp" #include "topol_C.itp" ;#ifdef POSRES ;#include "lipid_posre.itp" ;#endif ; Include water topology #ifdef FLEX_SPC #include "flexspc.itp" #else #include "spc.itp" #endif #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name PROTEIN IN DPPC BILAYER [ molecules ] ; Compound #mols Protein_A 1 Protein_B 1 Protein_C 1 DPPC 926 ;SOL 23552 Please help with some suggestions. Thanking you, Yours sincerely, Pawan On Mon, Mar 30, 2009 at 6:22 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > Pawan Kumar wrote: > >> Respected Sir, >> >> Greetings from Pawan. >> I did the Inflategro procedure for the POPC bilayer generated using >> genconf. >> It took around 26 compressions for coming near the initial area (just >> above it). >> The minimization were all converged to Fmax < 1350. >> If I decrease the Fmax less than this I am getting machine precision. >> But when I proceeded with the final compressed structure for pr mdrun it >> gave lincs warnings and ended with segmentation fault. >> As an alternative to this bilayer I used the DPPC bilayer >> (pre-equilibrated) which is given in GMX-Benchmark distribution. >> I carried out the same steps of Inflategro. I used the cutoff of 14 A in >> the inflation and compression step also. >> In this case the the Steepest Descents converged to Fmax < 1000 in all the >> steps. The maximum force war never above 850. >> 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). >> Can you please help how to proceed ? >> >> > 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. > > -Justin > > Thanking you, >> >> Yours sincerely, >> Pawan >> >> >> Justin A. Lemkul >> Graduate Research Assistant >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >
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