Hi, Sorry for the incomplete details. Here they are now:
I started with a well-equilibrated POPC bilayer, and changed one POPC lipid to a lipid of my interest. I wrote the topology file for the new lipid accordingly. After that, I did some simple steepest descent minimization, and followed it up by dynamics. Here is the .mdp file for the runs. There is a preceding 25,000-step simulation where the initial velocities are assigned. The mdp file below is what is being used for equilibrium dynamics. thank you for the suggestions. I will also explore the archives ; ; Input file ; ;------------------------- ; BASICS ;------------------------- title = dummy-file cpp = /usr/bin/cpp integrator = md tinit = 0 init_step = 25000 nsteps = 100000 dt = 0.002 ;------------------------- ; BOND PARAMETERS ;------------------------- constraints = hbonds constraint_algorithm = lincs unconstrained_start = yes lincs_order = 4 lincs_warnangle = 30 ;------------------------- ; OUTPUT CONTROL ;------------------------- nstxout = 5000 ; positions nstvout = 5000 ; velocity nstlog = 5000 ; energies to log file nstenergy = 5000 ; energy to energy file ;------------------------- ; MISCELLANEOUS ;------------------------- comm_mode = linear nstlist = 10 ns_type = grid pbc = xyz ; ------------------ ; NONBONDED INTERACTIONS ; ------------------ coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rlist = 1.0 rvdw = 1.0 fourierspacing = 0.1 pme_order = 4 ewald_rtol = 1e-5 ; --------------------------- ; NPT ; --------------------------- Tcoupl = berendsen tc-grps = LIP Solvent tau_t = 0.1 0.1 ref_t = 313.0 313.0 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; --------------------------- gen_vel = no ; --------------------------- On Fri, Apr 4, 2008 at 6:44 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>: > > > Quoting maria goranovic <[EMAIL PROTECTED]>: > > > > > Dear All > > > > > > I am running a 128-lipid bilayer simulation with standard parameters. > The > > > simulation abruptly crashed after 2 ns, and a look into the pdb files > > > suggested that bonds were being broken and eventually the lipids > explode. I > > > tried increasing the cutoffs from 1.0 to 1.4, and this time also, the > > > simulation exploded, but at a different time point. > > And as an aside, broken bonds are only a visualization effect; mdrun > doesn't > write broken molecules. Also, providing your .mdp file would be of use. > > -Justin > > > > > > > The energy remains nice and stable till the explosion. > > > > > > How does one fix this ? What is planting these bombs ? > > > > You'll have to describe how you minimized and equilibrated your bilayer > > before > > we'll have any idea what's going on. Also have a thorough look through > the > > archives; many users have posted about bilayers exploding (including > yours > > truly). > > > > -Justin > > > > > > > > Thank you for suggestions. > > > > > > -- > > > Maria G. > > > Technical University of Denmark > > > Copenhagen > > > > > > > > > > > ======================================== > > > > Justin A. Lemkul > > Graduate Research Assistant > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > [EMAIL PROTECTED] | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > > > ======================================== > > > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Maria G. Technical University of Denmark Copenhagen
_______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php