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"
#else
#include "spc.itp"
#endif
[ 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
well???
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
btm.mdp
Description: Binary data
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