[gmx-users] Re: gmx-users Digest, Vol 37, Issue 18

Arun kumar arun.target at gmail.com
Sat May 5 07:34:26 CEST 2007

Hi Tsjerk and gmx-users,
                        Thank you for the response. And I will be more
clear in asking questions.  The force field I am using is ffgmx. I am
not sure I will obtain good properties for my system with ffgmx at
this time. But I want to understand how to set up my simulation which
contains ionic surfactants.

                        And yes I will strat it for one surfactant and
one counterion in water.

                        In my post, MDRUN means True dynamics( I mean
real md not energy minimization). I know that without minimizing the
energy it will be bad to do MD. But I just checked how it will work as
I kept density around 330 kg/m^3. I think it won't work even. Sorry
for confusing with last post.

                       My system's initial configuration is alright it
seems(No overlapping atoms and bonds). And after I start EM or MD it's
exploding(Why I don't know exactly).

                       Now I will tell the steps I took to start my
simulation. Initially I got topology and pdb files(united atom) from
PRODRG(gromos 87 force field) for my surfactant behenyl(C22) trimethyl
ammonium chloride(charge +1, it won't contain chloride) and stearyl
alcohol. And then I got water.pdb,chlorine.pdb from pdb database. I
prepared a random configuration of 1400 water molecules, 20 surf, 20
chloride ions and 40 co-surfs in 5X5X8 nm^3 by using packmol.

                      Then I used editconf to get system.gro from
system.pdb and also put in a cubic box with this command
                  editconf -f system.pdb -bt cubic -o system.gro

                  But it reported system volume was zero. So I changed
end of my .gro file by replacing 0.0000 0.0000 0.0000  by 5.000 5.000
8.000. The density is about 330 kg/m^3. So I thought it will be useful
in Energy Minimization and also can be adjusted in NPT md simulation.
As i have a little experience in DPPC topologies and running
simulation for DPPC bilayer phase(successfully) using the files got
from Tieleman's website, I prepared a topology file for my
system(btm.top). It contains the following lines

#include "ffgmx.itp"
#include "btm87.itp"
#include "stearyl87.itp"
#include "ions.itp"

#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"
[ system ]
BTM with cosurf
[ molecules ]
; name	number
BTM       20
STR 	  40
SOL     1400
Cl 	   20

btm87.itp(surf) and stearyl87.itp(co-surf) are topologies got from PRODRG.

           I kept all these in my direactory. Now I tried to minmize
the energy of the system. First I used grompp to create md input
file(I mean for EM). It worked fine. But for mdrun system is
exploding(for l-bfgs method). For steepest descent it's not,  But the
potential energy of the system was a big positive number at end. For
my true MD also the system's exploding like l-bfgs minmization after
showing that warning earlier I posted. These are the steps I took  and
results I got. And for last query regarding tc-grps, I coupled the
whole system to a heat bath at 300 K. I observed the previous posts.
Here with this mail I attached my MD .mdp file.

         And at last Is there any relation with Mark's(Mark abraham)
observations regarding broken topologies in some of the posts I
observed, with my problem. Can anyone explain what is meant by a
broken topology file.  Try to help me to understand these thing
I can give any more details if it is needed.

Thanks and regards
Arun Kumar
M.E chem engg

> Hi Arun,

> You have to get your methods straight.., and be more clear in the
> phrasing of your question.
> >                          I am trying to simulate a surfactant-water
> > system(also contains some co-surfactants).  Surfactant is a cationic
> > surfactant with chloride as counterion. And the cosurfactant is fatty
> > alcohol. water is of spc model. I got topologies from Prodrg for my
> > surfactant and cosurfactant.
> What force field do you use? The standard output from PRODRG for
> gromacs is the gmx force field, which is deprecated and shouldn't be
> used (this is in the archives).
> > So  I  minimized the energies  for both my
> > molecules. And prepared a system of 1400 waters, 20 surfactants, 20 counter
> > ions and 40 cosurfactants in a box  of 5X5X8 nm^3 using packmol.
> >
> Maybe you're better of trying one surfactant molecule and one chloride
> in water to start with?
> >                         I tried to minimize the energy of the system using
> > l-bfgs. But I am always getting the error attached below. In my em.mdp file
> > I am using pme for coulomb type.  Even for MDRUN also I am getting the same
> > error...  I checked the previous posts and I am unable to understand what's
> > the problem. And can anyone tell what is meant by broken topology??? Also
> > try to help me to get out of the problem.
> Even for MDRUN? pfff, that must be really bad then. First of all, do
> you mean running the program 'mdrun' with the .tpr file for l-bfgs EM,
> or an actual MD run? In case of the latter, wouldn't you think there's
> little point in starting an MD run if energy minimization already
> failed? In case of the former, the statement is redundant (now it's
> just confusing).
> >     F-max             =          inf on atom 97
> >     F-Norm            =          nan
> >  -----------
> So, your system is exploding... Do you have any overlapping
> bonds/atoms? Does your box actually contain your system? (Do think
> periodically..., overlapping periodic images?).
> >
> >  My topology contains a system of four types surfactant, cosurfctant, water
> > and Chloride ions. Until grompp everything is fine. Total charge on system
> > is zero. I can give any more details if it is needed.
> Good, until grompp everything's fine. Now, then the error comes as a
> surprise! But what did you do before? What steps did you take?
> Oh, and I bet that in your .mdp file it says "tc-grps = SOL SUR ALC
> CL", albeit that the actual names and the order of them may be
> different. This is an issue, which has also been dealt with
> extensively (including the past week). In any case, when reporting
> that you've ran into a problem, it may be helpful to us to send your
> .mdp file.
> Cheers,
> Tsjerk
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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