[gmx-users] Density profile

[Justin Lemkul]

On 4/29/16 11:08 AM, Ashutosh Akshay Shah wrote:
> Alexander,
>
> For question 1.
> -b 500 gives a time average density for 500ps or 0.5ns. If you change it to
> 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.

-Justin

> Regards,
> Ashutosh Shah
>
> On Friday, April 29, 2016, Alexander Alexander <alexanderwien2k at gmail.com>
> wrote:
>
>> 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 simulation
>> applid.
>>
>> 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 this
>> 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 500
>> -o HWdens.xvg
>>
>> 2. What is the "Relative density profile" which I see in some publications
>> 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,
>> Regards,
>> Alex
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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================