[gmx-users] Regarding g_wham options
Nitin Agrawal
nitinyugalagrawal at gmail.com
Wed May 30 15:30:56 CEST 2012
Ok, Thank you once again.
On Wed, May 30, 2012 at 4:20 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 5/30/12 9:17 AM, Nitin Agrawal wrote:
>
>> I got this by using the command :
>>
>> g_wham -b 5000 -zprof0 -2.0 -it tpr_files.dat -if pullf_files.dat -o
>> profile_new1.xvg -hist histo_new1.xvg -unit kCal
>>
>> is their any way to shift the 0 in the y axis so it corresponds to -2 in
>> the
>> x-axis. It is just to make the graph look neater and the calculations to
>> become
>> easier
>>
>>
> That's precisely what your command is doing.
>
> The data in the PMF curve are dependent upon how the umbrella sampling
> calculations were conducted. There is no way to manipulate the positions
> of values along the curve, nor should you want to. The -zprof0 option
> simply allows you to choose a convenient reference point, since free energy
> is calculated as the difference between two states. Any further
> manipulation would be spurious.
>
> -Justin
>
>
>> On Wed, May 30, 2012 at 4:08 PM, Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>> On 5/30/12 8:57 AM, Nitin Agrawal wrote:
>>
>> How can I define the value at y axis then? Is there any way to
>> bring the
>> y-axis
>> value down to 0?
>>
>>
>> You want the energy minimum to be equal to zero, correct? This is
>> nothing
>> more than a reference point, so the value passed to -zprof0 is the
>> coordinate value (x-axis) at which the energy minimum occurs. Setting
>> a
>> proper value will shift the curve such that the energy minimum is at
>> zero.
>>
>> -Justin
>>
>> On Wed, May 30, 2012 at 3:24 PM, Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>>
>>
>>
>> On 5/30/12 8:18 AM, Nitin Agrawal wrote:
>>
>> When I am using the command -zprof0. it is not giving the
>> desired
>> result. I am
>> using it as
>>
>> g_wham -b 5000 -zprof0 -6.0 -it tpr_files.dat -if
>> pullf_files.dat -o
>> profile_new1.xvg -hist histo_new1.xvg -unit kCal
>>
>> but the lowest point in the graph is still -6.0 in the y
>> axis
>> and not
>> set to 0.0
>>
>> Am i using the parameters wrong?
>>
>>
>> >From g_wham -h:
>>
>> "-zprof0 real 0 Define profile to 0.0 at this position
>> (with -log)"
>>
>> The value provided should be the point along the x-axis (the
>> reaction
>> coordinate) where you want the value of the PMF (on the
>> y-axis) to
>> be zero.
>> Your original plot only contained values between about -2 and
>> 2, so
>> specifying -6 is not valid.
>>
>> -Justin
>>
>> On Wed, May 30, 2012 at 1:42 PM, Nitin Agrawal
>> <nitinyugalagrawal at gmail.com <mailto:nitinyugalagrawal@**gmail.com<nitinyugalagrawal at gmail.com>
>> >
>> <mailto:nitinyugalagrawal at __gm**ail.com <http://gmail.com><mailto:
>> nitinyugalagrawal@**gmail.com <nitinyugalagrawal at gmail.com>>>
>> <mailto:nitinyugalagrawal@ <mailto:nitinyugalagrawal@>__g**
>> m__ail.com <http://gm__ail.com>
>> <http://gmail.com>
>>
>>
>> <mailto:nitinyugalagrawal at __gm**ail.com <http://gmail.com>
>> <mailto:nitinyugalagrawal@**gmail.com<nitinyugalagrawal at gmail.com>>>>>
>> wrote:
>>
>> Thank you
>>
>>
>> On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul
>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu> <mailto:
>> jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>>>> wrote:
>>
>>
>>
>> On 5/30/12 6:29 AM, Nitin Agrawal wrote:
>>
>> Hi all,
>>
>> I want to set the lowest point in my curve as
>> zero
>> instead of
>> negative number.
>> Can anyone tell me which option to use to do
>> that?
>>
>>
>> Set the desired value with -zprof0.
>>
>> -Justin
>>
>> --
>> ==============================**______==========
>>
>>
>>
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu>
>> <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.__**____vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin>
>> <http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin>
>> >
>> <http://vt.edu/Pages/Personal/**__justin<http://vt.edu/Pages/Personal/__justin>
>> <http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin>
>> >>
>>
>> <http://www.bevanlab.biochem._**___vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin>
>> <http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin>
>> >
>> <http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin
>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >>**>
>>
>> ==============================**______==========
>>
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>**>
>> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>**>__>
>> http://lists.gromacs.org/_____**_mailman/listinfo/gmx-users<http://lists.gromacs.org/______mailman/listinfo/gmx-users>
>> <http://lists.gromacs.org/____**mailman/listinfo/gmx-users<http://lists.gromacs.org/____mailman/listinfo/gmx-users>
>> >
>>
>> <http://lists.gromacs.org/____**mailman/listinfo/gmx-users<http://lists.gromacs.org/____mailman/listinfo/gmx-users>
>> <http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>> >>
>>
>>
>> <http://lists.gromacs.org/____**mailman/listinfo/gmx-users<http://lists.gromacs.org/____mailman/listinfo/gmx-users>
>> <http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>> >
>> <http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> >>>
>> Please search the archive at
>> http://www.gromacs.org/______**Support/Mailing_Lists/Search<http://www.gromacs.org/______Support/Mailing_Lists/Search>
>> <http://www.gromacs.org/____**Support/Mailing_Lists/Search<http://www.gromacs.org/____Support/Mailing_Lists/Search>
>> >
>>
>> <http://www.gromacs.org/____**Support/Mailing_Lists/Search<http://www.gromacs.org/____Support/Mailing_Lists/Search>
>> <http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search>
>> >>
>>
>>
>> <http://www.gromacs.org/____**Support/Mailing_Lists/Search<http://www.gromacs.org/____Support/Mailing_Lists/Search>
>> <http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search>
>> >
>> <http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search>
>> <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>
>> >>**> before posting!
>> Please don't post (un)subscribe requests to the
>> list.
>> Use the www
>> interface or send it to
>> gmx-users-request at gromacs.org
>> <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >
>> <mailto:gmx-users-request at __gr**omacs.org <http://gromacs.org>
>> <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >>
>> <mailto:gmx-users-request@ <mailto:gmx-users-request@>__g**
>> r__omacs.org <http://gr__omacs.org>
>> <http://gromacs.org>
>>
>>
>> <mailto:gmx-users-request at __gr**omacs.org <http://gromacs.org>
>> <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >>>.
>> Can't post? Read
>> http://www.gromacs.org/______**Support/Mailing_Lists<http://www.gromacs.org/______Support/Mailing_Lists>
>> <http://www.gromacs.org/____**Support/Mailing_Lists<http://www.gromacs.org/____Support/Mailing_Lists>
>> >
>>
>> <http://www.gromacs.org/____**Support/Mailing_Lists<http://www.gromacs.org/____Support/Mailing_Lists>
>> <http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>> >>
>>
>>
>> <http://www.gromacs.org/____**Support/Mailing_Lists<http://www.gromacs.org/____Support/Mailing_Lists>
>> <http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>> >
>> <http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>> >>>
>>
>>
>>
>>
>> --
>> Regards,
>> Nitin Agrawal,
>> Master's Student (Bioinformatics)
>> University of Turku,Finland
>> B.Tech (Biotechnology)
>> National Institute of Technology,Durgapur,India
>> Blog:http://____**notjustanyotherblog.blogspot._**
>> ___com/
>>
>> <http://notjustanyotherblog.__**blogspot.com/<http://blogspot.com/>
>>
>> <http://notjustanyotherblog.**blogspot.com/<http://notjustanyotherblog.blogspot.com/>
>> >>
>>
>>
>>
>>
>> --
>> Regards,
>> Nitin Agrawal,
>> Master's Student (Bioinformatics)
>> University of Turku,Finland
>> B.Tech (Biotechnology)
>> National Institute of Technology,Durgapur,India
>> Blog:http://____**notjustanyotherblog.blogspot._**___com/
>> <http://notjustanyotherblog.__**blogspot.com/<http://blogspot.com/>
>> <http://notjustanyotherblog.**blogspot.com/<http://notjustanyotherblog.blogspot.com/>
>> >>
>>
>>
>>
>>
>> --
>> ==============================**____==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>> 231-9080
>> http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin
>> <http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin>
>> >
>> <http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin
>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >>
>>
>> ==============================**____==========
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>**>
>> http://lists.gromacs.org/____**mailman/listinfo/gmx-users<http://lists.gromacs.org/____mailman/listinfo/gmx-users>
>> <http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>> >
>> <http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> >>
>> Please search the archive at
>> http://www.gromacs.org/____**Support/Mailing_Lists/Search<http://www.gromacs.org/____Support/Mailing_Lists/Search>
>> <http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search>
>> >
>> <http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search>
>> <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>>
>> before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www
>> interface
>> or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >
>> <mailto:gmx-users-request at __gr**omacs.org <http://gromacs.org>
>> <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >>.
>> Can't post? Read http://www.gromacs.org/____**
>> Support/Mailing_Lists <http://www.gromacs.org/____Support/Mailing_Lists>
>> <http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>> >
>> <http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>> >>
>>
>>
>>
>>
>> --
>> Regards,
>> Nitin Agrawal,
>> Master's Student (Bioinformatics)
>> University of Turku,Finland
>> B.Tech (Biotechnology)
>> National Institute of Technology,Durgapur,India
>> Blog:http://__**notjustanyotherblog.blogspot._**_com/
>> <http://notjustanyotherblog.**blogspot.com/<http://notjustanyotherblog.blogspot.com/>
>> >
>>
>>
>> --
>> ==============================**__==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
>> ==============================**__==========
>> --
>> gmx-users mailing list gmx-users at gromacs.org <mailto:
>> gmx-users at gromacs.org>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> >
>> Please search the archive at
>> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search>
>> <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>
>> before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface
>> or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >.
>> Can't post? Read http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>> >
>>
>>
>>
>>
>> --
>> Regards,
>> Nitin Agrawal,
>> Master's Student (Bioinformatics)
>> University of Turku,Finland
>> B.Tech (Biotechnology)
>> National Institute of Technology,Durgapur,India
>> Blog:http://**notjustanyotherblog.blogspot.**com/<http://notjustanyotherblog.blogspot.com/>
>>
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
--
Regards,
Nitin Agrawal,
Master's Student (Bioinformatics)
University of Turku,Finland
B.Tech (Biotechnology)
National Institute of Technology,Durgapur,India
Blog:http://notjustanyotherblog.blogspot.com/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120530/860899cb/attachment.html>
More information about the gromacs.org_gmx-users
mailing list