[gmx-users] Density profile
alexanderwien2k at gmail.com
Fri Apr 29 17:23:15 CEST 2016
Thanks for your response.
That I know, the problem is not with "-b" as it clear that with "-b 500",
the first 500 frame will be discarded from analysing.
But, I am still looking forward to hearing more from you.
On Fri, Apr 29, 2016 at 5:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 4/29/16 11:08 AM, Ashutosh Akshay Shah wrote:
>> For question 1.
>> -b 500 gives a time average density for 500ps or 0.5ns. If you change it
>> 5000, it'll show the time average density for 5ns and the graph will be
>> much smoother.
> That's not correct. The -b option is the starting point for analysis.
> With -b 500, you'll get analysis over 500 - 5000 ps. With -b 5000, you'll
> get nothing in this instance.
>> Ashutosh Shah
>> On Friday, April 29, 2016, Alexander Alexander <alexanderwien2k at gmail.com
>> Dear Gromacs user,
>>> My system is a metal surface with thousands of Water molecule on it,
>>> normally surface(3 nm) is in the bottom of the box and the rest on top is
>>> water(6 nm). My target is to plot "density profile" of either WATER or OW
>>> or HW along to Z(Normal distance above solid surface); 5 ns NVT
>>> 1. "gmx density" has offered many options, I am not sure which I have to
>>> choose to do so for this system, so, what is the right command to get
>>> density profile:
>>> Mine is below , would you please improve it? I do not know why mine is
>>> never like what I see in publications.
>>> gmx density -f nvt.trr -s nvt.tpr -n surf-sol.ndx -d Z -dens number -b
>>> -o HWdens.xvg
>>> 2. What is the "Relative density profile" which I see in some
>>> usually? Relative to what it is?
>>> 3. What is the difference between "radial distribution function" and
>>> "density profile" especially for such a goal?
>>> Thanks in advance,
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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