Vitaly Chaban wrote:
Dear Gmx-users,
I am simulating a carbon nanotube in vaccum (NVE ensemble). I have taken
parameters of carbon nanotube from "Strong correlations and Fickian
water water
diffusion in narrow carbon nanotube, Biswaroop Mukherjee, Prabal K.
Maiti Chandan
Dasgupta and A. K. Sood, JCP, 126 124704 (2007)".
During the run my carbon nanotube does not remain cylindrical, it
bends inwards and forms
a dumbell shaped structure, also it rotates in space and does not
remain fixed.
My questions are
1) are my itp and mdp parameters correct
Formally correct.
Flexible water should not be used for MD.
what do you mean?
http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html
All the water models in Gromacs
should be rigid. As such, "define = -DFLEXIBLE" is incorrect.
where did water come from? he said "I am simulating a carbon nanotube
in vaccum (NVE ensemble)"
Sorry, missed that part. I saw the "define" line and assumed some incorrect
treatment of water. I guess that probably invalidates my point below, as well.
-Justin
2) how do i determine if system is really in ground state or stable
You CNT should not migrate within a box, for sure. I believe it is
principally impossible in spite of the force field parameters that can
be used. You may want to upload the video with the system dynamics on
the YOUTUBE for us to look at.
3) temprature keeps on rising as the simulation proceeds is this all
right?
No. For how much does it increase?
Using a plain cutoff for the electrostatics could be causing this.
-Justin
--
Dr. Vitaly Chaban
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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