[gmx-users] Regarding g_wham options

[Nitin Agrawal]

How can I define the value at y axis then? Is there any way to bring the
y-axis value down to 0?

On Wed, May 30, 2012 at 3:24 PM, Justin A. Lemkul <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>>>
>> wrote:
>>
>>    Thank you
>>
>>
>>    On Wed, May 30, 2012 at 1:39 PM, Justin A. Lemkul <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> | (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/>
>>
>>
>>
>>
>> --
>> 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/20120530/810b9b07/attachment.html>