[gmx-users] g_wham 4.6.7 version output query

Agnivo Gosai agnivogromacs14 at gmail.com
Mon Dec 8 21:35:03 CET 2014

Hi Users

I googled on the issue and found the following :


In the above mentioned link an user had previously wrote about the
creation of this pmfintegrated.xvg file and as mentioned it is not
being created all the time..

I also found the following from the source code of 4.5.5. version

if (opt->verbose)
        fp=xvgropen("pmfintegrated.xvg","PMF from force
integration","z","PMF [kJ/mol]",opt->oenv);
            fprintf(fp,"%g  %g\n",(j+0.5)*dz+opt->min,pot[j]);
        printf("verbose mode: wrote %s with PMF from interated

However I am using version 4.6.7. And I also use -v in the command
line for g_wham as indicated in the trailing mail. Can someone say
what is going on. Lookwise the  pmfintegrated.xvg is so smooth that I
am tempted to use it , but I don not know why and how it is generated.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

On Mon, Dec 8, 2014 at 11:35 AM, Agnivo Gosai <agnivogromacs14 at gmail.com>

> Dear Users
> I am doing an umbrella sampling following the Lemkul tutorial. I noticed
> that while using g_wham for the 1st time in 2 of my study cases I get as an
> output a file called pmfintegrated.xvg.
> My command line is
> g_wham_d -it tpr-files.dat -if pullf-files.dat -o PMF.xvg -hist
> HISTOGRAM.xvg -unit kCal -v
> I get the PMF.xvg having unit of energy as kCal/mol and due to improper
> sampling as evident from the Histogram plot , my PMF profile is having
> discontinuities.
> However , automatically , another file got generated whose energy unit is
> kJ/mol , also the plot is a lot smoother and without any discontinuity. I
> checked the GROMACS 4.6.7 manual and am feeling confused as there is no
> mention of this output.
> I am including all the images. PMF1 = Case 1 , PMF2 = Case 2 and
> pmfintegrated.png contains both the cases.
>>  PMF1.png
> <https://docs.google.com/file/d/0B-U8uULVZjfRMVRINHNQOURCOWc/edit?usp=drive_web>
> ​​
>  PMF2.png
> <https://docs.google.com/file/d/0B-U8uULVZjfRWXdXVGVlNXU3Rm8/edit?usp=drive_web>
> ​​
>  pmfintegrated.png
> <https://docs.google.com/file/d/0B-U8uULVZjfROVBaaGlxWThZdEk/edit?usp=drive_web>
>> Kindly explain the possible reason behind this.
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.

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