[gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode

[maria goranovic]

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 <jalemkul at vt.edu> wrote:

> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
> > Quoting maria goranovic <mariagoranovic at gmail.com>:
> >
> > > 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
> > jalemkul at vt.edu | (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
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Maria G.
Technical University of Denmark
Copenhagen
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080407/71757b29/attachment.html>