it is better to avoid rotation at this initial stage. if you
experience certain features in your finals PMFs which you cannot
explain, you will always be unsure where they arrive from. this hurts
your soul.
Dr. Vitaly V. Chaban
On Thu, May 29, 2014 at 9:41 PM, ANDRES ADOLFO ORTEGA GUERRERO
wr
On 5/29/14, 3:41 PM, ANDRES ADOLFO ORTEGA GUERRERO wrote:
Should i try instead different pull MD(changing the pbcatom, CNT's COM,
velocity,force) , in order to get new configuration for an umbrella
sampling simulation and a PMF in z Axis calculation, until i´ll get no
rotation in the CNT?
The
Should i try instead different pull MD(changing the pbcatom, CNT's COM,
velocity,force) , in order to get new configuration for an umbrella
sampling simulation and a PMF in z Axis calculation, until i´ll get no
rotation in the CNT?
or can i used this MD, to get the configuration for the Umbrella Sa
On 5/28/14, 12:11 PM, ANDRES ADOLFO ORTEGA GUERRERO wrote:
Thank you Justin For the Help,
I was wondering should i use a stronger force?,
My idea is to get the PMF of the SWCNT getting closer to the ion channel,
should i run a diferent pull MD in order to get hte configuration for the
umbrell
Thank you Justin For the Help,
I was wondering should i use a stronger force?,
My idea is to get the PMF of the SWCNT getting closer to the ion channel,
should i run a diferent pull MD in order to get hte configuration for the
umbrella sampling , or should i try a different force, or just put the
provided that pulling forces are normally selected (much) larger than
the genuine forces in the simulated system, unfavorable interactions
are unlikely to cause the observed effect. however, rotation is
probably somehow geared by pulling energy. i looked though the movie -
it is like a nice helicop
On 5/27/14, 11:25 AM, ANDRES ADOLFO ORTEGA GUERRERO wrote:
Hi Dr Vitaly ,
First 3nm it is not half of any side, i used the external amino acids from
the channel as a reference gruop, and 3nm is the distance from the SWCNT
tip's to the channel, but 6nm from the COM, my box has 19 nm in Z axis,
Hi Dr Vitaly ,
First 3nm it is not half of any side, i used the external amino acids from
the channel as a reference gruop, and 3nm is the distance from the SWCNT
tip's to the channel, but 6nm from the COM, my box has 19 nm in Z axis,
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This sounds too crazy for me.
Do you have an image of your MD box?
What does 3nm mean for your box? Half of any side?
Dr. Vitaly V. Chaban
On Mon, May 26, 2014 at 8:56 PM, ANDRES ADOLFO ORTEGA GUERRERO
wrote:
> Hi dear Gromacs User,
> I have done a pulling simulation of a SWCNT against an ion
Hi dear Gromacs User,
I have done a pulling simulation of a SWCNT against an ion channel(the
SWCNT , and the ion channel pore's are the same), in order to study
the interaction between SWCNT and the outside (extracellular side) of the
channel,
So i put the SWCNT about 3nm of distance from the ion c
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