On 2/23/15 3:47 AM, Peter Kroon wrote:
On 02/22/2015 05:33 PM, Jashimuddin Ashraf wrote:
Thanks for your reply Dr. Lemkul
I changed the bond length to zero in my topology file, forcefield file
and
in the n2t file. I also added the [ exclusion] section-
If memory serves, you don't need a bond between a shell particle and
it's "parent"; the polarization directive takes care of it's position.
If you want, you can define a non-interacting connection (bond type 5)
between them.
This is correct. The [polarization] directive is just another bonded
interaction. The value of the force constant is back-calculated from
the
atomic polarizability, alpha.
[ exclusions ]
; iatom excluded from interaction with i
1 2 3 4 5 6 7 8
2 1 3 4 5 6 7 8
3 1 2 4 5 6 7 8
4 1 2 3 5 6 7 8
5 1 2 3 4 6 7 8
6 1 2 3 4 5 7 8
7 1 2 3 4 5 6
8 1 2 3 4 5 6
in my topology. But the same error keeps showing up. What did I
possibly
do
wrong?
AFAIK this will exclude all atoms from eachother. Just the last line
should be enough if you just want to exclude the shell-carbon
interactions
In your mail, you were kind to reply with-
"I only looked at the paper briefly, but it seems they are working
with a
model that makes use of anisotropic polarization. In GROMACS, this is
currently only available for water, so the model would not be
supported."
Are you suggesting that, this model is something we should not work
with
in
GROMACS right now? (I am really sorry, I could not understand this
part
properly)
From my quick read of the paper (focusing only a narrow section of
the
methods), the authors list alpha_zz only, implying that the shell is
only
polarizable along the normal to the ring. Therefore the other elements
of
the polarization tensor are zero.
Also, it would be very nice, if you could give us an idea about the
time
required to publish the codes and adding them in the new versions of
GROMACS.
That depends on reviewers :)
The paper should be submitted this week, after which I will be working
to
submit the code to the master development branch. The code will not be
included in 5.1 (I missed the deadline, due to some debugging that took
longer than expected), but the code will be available as a patch to the
master branch in the coming weeks.
-Justin
Thanks in advance,
Lastly, for defining the virtual site you could look at the
virtual_sitesn directives and define a center of geometry or a center
of
mass. Im not sure if it has any advantages over a virtual site as it is
defined now though.
If your simulation blows up, try analysing the distance between the
shell and it's parent; it should give you a hint about what's going
wrong.
Good luck!
Regards,
Peter Kroon
On Sat, Feb 21, 2015 at 12:20 AM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 2/20/15 12:57 PM, Jashimuddin Ashraf wrote:
Dear users,
I want to perform a molecular dynamic simulation of polarizable
carbon
nanotubes. I intend to implement this paper-
http://www.sciencedirect.com/science/article/pii/S0927025607000456
I digged up the manual but could not find much help from it. I went
through
some mails in the gromacs user maillist, studied some .itp files and
learned some elementary stuffs regarding the addition of virtual
sites
and
shell atoms.I understand that I have to add both shell and virtual
sites
in
this case.
Now, before jumping right into a big nanotube molecule, I was
trying to
perform a simulation with a single benzene ring with a virtual site
placed
at the center and a shell attached to the virtual site.
In my forcefield.itp file have the virtual site and the shell
declared
like
this-
------------------------------------------------------------
------------------------------------------------------------
-------------
[ atomtypes ]
; name mass charge ptype sigma eps
CJ1 1 12.01100 0.25 A 3.40000e-01 3.60100e-01
VS 1 0 0 D 0 0
SL 1 0 -1.5 S 0 0
[ bondtypes ]
`; i j func b0 kb gamma
CJ1 CJ1 3 0.1418 478.9000 21.867
VS SL 1 0.06 2409
------------------------------------------------------------
------------------------------------------------------------
-------------
Here, I have considered a bond between the virtual site and the
shell
(the
paper mentions something like it but does not provide with the bond
length). Is it a mistake?
The equilibrium bond length should be zero (i.e. no induced
polarization).
and inside my topol.top file, I have-
------------------------------------------------------------
------------------------------------------------------------
-------------
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 CJ1 1 C C 1 0.25
12.011 ;
qtot 0.25
2 CJ1 1 C C 1 0.25
12.011 ;
qtot 0.5
3 CJ1 1 C C 1 0.25
12.011 ;
qtot 0.75
4 CJ1 1 C C 1 0.25
12.011 ;
qtot 1.00
5 CJ1 1 C C 1 0.25
12.011 ;
qtot 1.25
6 CJ1 1 C C 1 0.25
12.011 ;
qtot 1.50
7 VS 1 C VS 1 0 0
;
qtot 1.50
8 SL 1 C S 1 -1.5
0
;
qtot 0
[ polarization ]
; virtual_site shell functiontype alpha (in nm^3)
7 8 1 0.1
I only looked at the paper briefly, but it seems they are working
with a
model that makes use of anisotropic polarization. In GROMACS, this
is
currently only available for water, so the model would not be
supported.
It will be soon (I know I've been saying that for a while, but our
paper
regarding Drude simulations in GROMACS is just about done, after
which I
can provide the code).
[ bonds ]
; ai aj funct c0 c1 c2
c3
1 2 3
1 5 3
2 4 3
3 4 3
3 6 3
5 6 3
7 8 1
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
5 1 2 4 3
2 1 5 6 3
1 2 4 3 3
6 3 4 2 3
4 3 6 5 3
1 5 6 3 3
[ virtual_sites3 ]
; detailed calculation not shown here
; Dummy from funct a b
7 4 5 6 1 0.5 0
You're missing a critical element here; the paper says that the
shell
does
not interact with the carbon atoms of the ring, so you need to define
exclusions manually.
-Justin
------------------------------------------------------------
------------------------------------------------------------
-------------
I ran an energy minimization for an emtol of 100 but it gives me a
result
like this-
Steepest Descents converged to machine precision in 141 steps,
but did not reach the requested Fmax < 100.
Potential Energy = -6.1810545e+06
Maximum force = 9.1656689e+12 on atom 4
Norm of force = 4.5828344e+12
------------------------------------------------------------
------------------------------------------------------------
-------------
If I run a production MD with this, the simulation blows up with
this-
MDStep= 40/18 EPot: nan, rmsF: nan
Warning: Only triclinic boxes with the first vector parallel to the
x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
MDStep= 40/19 EPot: nan, rmsF: nan
step 40: EM did not converge in 20 iterations, RMS force nan
------------------------------------------------------------
------------------------------------------------------------
-------------
Is something wrong with my system itself? or is there anything wrong
with
my methods?
I have been stuck at this for a very long time now and anything- any
comment or hint would be very much helpful for me.
Thanks in advance,
Jashimuddin Ashraf
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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