Hi! Thanks for your suggestion on the tutorial. I will try it out. I actually tried to use the starting structure without going through editconf and alteration but it failed. Here's the error: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. I've tried on reducing the rlist but still failed. Please advice.
According to the tutorial you suggested, we are suppose to use genbox to solvate the membrane and remove those water manually by script that go inside the membrane. Does this mean that I'm suppose to throw away the water from the starting structure and resolvate it again? thanks again. regards, Bing On Tue, Jun 23, 2009 at 11:28 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Bing Bing wrote: > >> Thanks for reply. >> I've used editconf to define the box by issuing :- >> editconf -f popc.pdb -o popc_box.gro -c -d 1.0 -bt cubic >> Is this the correct way of using editconf? >> > > This would be appropriate for a protein, but not a membrane. What you're > doing is defining a layer of nothingness around the membrane/water system, > which may have molecules split across periodic boundaries. This could be > the reason everything is blowing up. > > Try running EM on the original, unaltered POPC from Tieleman's site. > > And with this i proceed with grompp with the mdp file from previous email >> followed by mdrun.... >> >> Actually the restraint is require in another system (membrane+protein), i >> wanted to test it out in the this smaller systme before using it in the >> complete systme.However, it failed. >> >> > Applying position restraints to every atom of a lipid in the presence of a > protein still serves little purpose. If you were to attempt to > energy-minimize such a system, the clashes (if any) between the protein and > lipids would go unresolved. Certainly equilibrating with such restraints > would be meaningless, as well. > > If you're interested, hopefully the tutorial here will help: > > http://oldwiki.gromacs.org/index.php/Membrane_Simulations > > It is designed for membrane protein simulations. > > -Justin > > Thanks in advance >> >> regards, >> bing >> >> >> On Tue, Jun 23, 2009 at 10:21 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Bing Bing wrote: >> >> Hi Justin, >> I've tried with no restraint and the minimization stopped at the >> same time. I actually suspect that the restraint is not working >> at all. My top file is as below:- >> #include "ffG53a6_lipid.itp" >> #include "popc.itp" >> #ifdef POSRES >> #include "posres_popc.itp" >> #endif >> #ifdef FLEX_SPC >> #include "flexspc.itp" >> #else >> #include "spc.itp" >> #endif >> >> [ system ] >> ; name >> Pure POPC bilayer with 128 lipids 2460 water >> >> [ molecules ] >> ; name number >> POPC 128 >> SOL 2460 >> >> my posres_popc.itp is as below:- >> [ position_restraints ] >> ; atom type fx fy fz >> 1 1 1000 1000 1000 >> ..... >> 51 1 1000 1000 1000 >> 52 1 1000 1000 1000 >> >> my mdp file as below :- >> define = -DPOSRES >> integrator = steep >> emtol = 1000 >> emstep = 0.01 >> nsteps = 100 >> rlist = 1.2 >> coulombtype = PME >> rcoulomb = 1.2 >> rvdw = 1.2 >> constraints = none >> >> May i know that is the top, posres and also the mdp file >> correctly done? >> >> >> Well, they are syntactically correct, it seems. I see no purpose in >> restraining lipids during a minimization, however. >> >> >> And by looking at the log file in the previous mail, is it >> confirm that it manage to read the restraint file? >> >> >> Can't tell. Your system is crashing instantly for some reason. >> >> >> The starting structure is taken from Peter Tielemen website and >> what i did is editconf to make box and i didn't solvate because >> the starting structure come together with water. I'm not sure >> this is the correct way of doing it. Please advice. >> >> >> Please define "editconf to make box" - have you somehow manipulated >> the structure? That could be a source of error. The structure that >> Tieleman provides minimized for me with no problem when I used it >> recently. >> >> -Justin >> >> >> >> Thanks in advance. >> Bing >> >> >> >> On Tue, Jun 23, 2009 at 7:16 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Bing Bing wrote: >> >> Hi! I'm a postgraduate student from Malaysia and currently >> facing energy minimization problem for my membrane system. >> I'm trying to perform energy minimization for an empty POPC >> membrane with position restraint on the lipid. >> Minimization stop >> due to inf Fmax. And I noticed that in the log file as >> below:- >> Initiating Steepest Descents >> Max number of connections per atom is 25 >> Total number of connections is 84976 >> Max number of graph edges per atom is 4 >> Total number of graph edges is 22896 >> Going to use C-settle (2460 waters) >> wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.08165, ra = >> 0.0384897 >> rb = 0.0192448, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH >> = 0.1 >> Started Steepest Descents on node 0 Tue Jun 23 17:03:43 2009 >> Steepest Descents: >> Tolerance (Fmax) = 1.00000e+03 >> Number of steps = 100 >> Grid: 11 x 11 x 11 cells >> Step Time Lambda >> 0 0.00000 0.00000 >> Energies (kJ/mol) >> Bond Angle Proper Dih. Ryckaert-Bell. >> Improper Dih. >> 1.64082e+05 1.71875e+04 4.06560e+03 >> 6.45104e+03 8.36392e+03 >> LJ-14 Coulomb-14 LJ (SR) Coulomb >> (SR) Coul. recip. >> 2.12067e-314 2.12067e-314 -1.58963e+04 >> -1.05392e+05 -1.15292e+05 >> Position Rest. Potential Pressure (bar) >> 0.00000e+00 -3.64297e+04 nan >> >> >> >From the looks of some of these energies (i.e., LJ-14, >> Coulomb-14), it looks like something is severely wrong with your >> starting structure, and applying position restraints probably >> isn't >> helping. >> >> Try the minimization without restraints and see if it works. >> >> Also, have you set the appropriate "define" line in the .mdp >> file, >> corresponding to what is prescribed in the .top? >> >> -Justin >> >> ------------------------------------------------------- >> Program mdrun_d, VERSION 4.0.5 >> Source code file: nsgrid.c, line: 357 >> Range checking error: >> Explanation: During neighborsearching, we assign each >> particle >> to a grid >> based on its coordinates. If your system contains >> collisions or >> parameter >> errors that give particles very high velocities you might >> end up >> with some >> coordinates being +-Infinity or NaN (not-a-number). >> Obviously, >> we cannot >> put these on a grid, so this is usually where we detect >> those >> errors. >> Make sure your system is properly energy-minimized and >> that the >> potential >> energy seems reasonable before trying again. >> Variable ci has value -2147483648. It should have been >> within [ >> 0 .. 1331 ] >> the position restraint energy is 0 as highlighted. >> Here's the >> position restraint file :- >> [ position_restraints ] >> ; atom type fx fy fz >> 1 1 1000 1000 5000 >> 5 1 1000 1000 1000 >> 6 1 1000 1000 1000 >> 7 1 1000 1000 1000 >> 8 1 1000 1000 1000 >> 9 1 1000 1000 1000 >> 10 1 1000 1000 1000 >> ...... >> >> whereby the restraint energy is 1000kcal/mol in x, y and z >> plane. In the log file the position restraint energy is >> stated >> as 0.0000e+00 (as highlighted above). >> I think that the position restraint is not working fine >> here. Is >> there anyways to solve this? did I miss out something here? >> I would be grateful if anyone can advice me on this. >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org >> >> >> >> http://lists.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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > 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://lists.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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