He, Yang wrote:
Hi Justin,
Yes, I am trying the course-grain model using gromacs, an absolute newer.
My current model is not complex, just including 22 big atoms, only 4 base pair.
What is the use of summing the entire base into one
particle?
The only coarse-grain FF I know anything about is MARTINI, which uses 4:1
mapping, i.e. 4 atoms represented by 1 particle. I would suspect that for 4
base pairs, one would have significantly more particles than 22 with this type
of mapping scheme. You may be missing some of the subtleties of the base pair
interactions by lumping a whole base into one particle.
The total charges are zero . And I just include water atoms and DNA strands in
my case. I guess maybe there is something wrong with their original positions.
I am trying to modify the coordinate.
Well, then you don't have DNA :) The backbone of DNA bears a negative charge at
physiological pH, and thus contributes to the overall stability (and somewhat to
the instability) of the helix. I would suggest refining your model a bit to
reflect the physiological model.
-Justin
Thank you for your further suggestions.
Yang
________________________________________
From: Justin A. Lemkul [EMAIL PROTECTED]
Sent: Tuesday, November 11, 2008 1:38 PM
To: He, Yang; Gromacs Users' List
Subject: Re: [gmx-users] the temperature effect in the simulation
He, Yang wrote:
Hi Justin,
In my case, my box size is adequate to avoid interaction of periodic images of
your DNA .For this point, I think is ok.
In fact, when I run this simulation especially for the low temperature, one
atom's(Tb1) behavior is strange .No matter how low the temperature is , it will
separate from the other matching pair . The others are normal.
It looks like you're working with some sort of coarse-grain model for DNA. If
you're developing new parameters, welcome to the headaches that come with such
derivations! Interaction between whatever Tb1 (thymine base?) and the other
atoms may need to be modified. Are you summing the entire base into one
particle? That's pretty extensive mapping that may not capture all the
H-bonding interactions, but I guess that's up to you to decide.
How about ions? Do you have a neutral solution, or do you have unsatisfied
charges from the backbone? That may affect the dynamics as well.
-Justin
I list my nb and bon file in the attachments .
Thank you
________________________________________
From: Justin A. Lemkul [EMAIL PROTECTED]
Sent: Tuesday, November 11, 2008 1:07 PM
To: He, Yang; Gromacs Users' List
Subject: Re: [gmx-users] the temperature effect in the simulation
He, Yang wrote:
Hi Justin,
My box size is 3.13690 3.73000 2.70000 and I use the user-defined
potential functions.
Is that box size adequate to avoid interaction of periodic images of your DNA?
Typical B-DNA is about 2 nm wide, if 2.7 nm is the width of your box, I'd bet
you're getting artefactual PBC interactions.
#define _FF_GROMACS
#define _FF_GROMACS1
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0
#include "ffyxhnb.itp"
#include "ffyxhbon.itp"
Well, if you're defining your own potential, I'd look there for spurious
repulsive terms. If the DNA is shearing apart, your repulsion between atoms may
be too large. Combine that with artefactual PBC interactions, and that may give
rise to your strange behavior.
This is my ffyxh.itp file
Also I have change the value of tau_t by 0.1 but it did not work.
Please let me know if you need any further information.
The entirety of the .mdp file, and what you've defined in your *nb.itp *bon.itp
files, in case there's anything obviously wrong.
-Justin
Thank you.
Yang
________________________________________
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL
PROTECTED]
Sent: Tuesday, November 11, 2008 12:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the temperature effect in the simulation
He, Yang wrote:
Hi all users,
When I change the temperature to try to get different disassociation about the
two DNA's strands. But even I change the value of temperature by 0K in the mdp
file ,
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = berendsen
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.001
ref_t = 300
I don't know if this is relevant or not, but a coupling constant of 0.001 is
exceptionally short. What is the timestep in your simulation? Typically one
sees tau_t = 0.1 with a timestep of 0.001-0.002 ps.
; Pressure coupling
Pcoupl = no
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
It will also disassociate .It is strange.
So the dissociation occurs at 0K and 300K? Sounds like something is
fundamentally flawed with your system setup. How large is your box? What force
field are you using?
-Justin
Can anyone of you tell me what is the reason for that?
Thank you in advance.
Yang
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--
========================================
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
========================================
_______________________________________________
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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]
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--
========================================
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
========================================
--
========================================
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
========================================
_______________________________________________
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