[gmx-users] Density profile

[Alexander Alexander]

Not really a specific publication I am comparing, but,in general I was
meaning.
Anyway,

do you know please why density profile differs a bit when "... -f case.trr
..." is used instead of "... -f case.xtc ..." in gmx density for a
simulation? Which one is preferred to use in this order?

Cheers,
Alex

On Fri, Apr 29, 2016 at 5:24 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/29/16 11:22 AM, Alexander Alexander wrote:
>
>> 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.
>>
>>
> RDF is explained in the manual.  If your results differ from those in
> publications or you don't understand what is presented in those papers,
> your questions should be directed to the authors, not this mailing list.
>
> -Justin
>
>
> Cheers,
>> Alex
>>
>> 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:
>>>
>>> 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
>>>>>
>>>>>
>>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>>
> --
> ==================================================
>
> 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
>
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