[gmx-users] error about g_bar

[Swapnil Kate]

hello Justin

 Thank you for your advice, that was really fruitful.

can you kindly tell me how to visualize the molecule which is appearing or disappearing (lamda 0 to 1, lamda 1 to 0 respectively)?

moving forward i am interested in calculating free energy of reacting mixtures so could you please tell me how to make a files and how to move forward?

Swapnil


On Wednesday, 13 August 2014 6:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 




On 8/13/14, 12:05 PM, Swapnil Kate wrote:
> hello justin,
>
> i used g_bar -b 100 -f lamda_0/dhdl.xvg -o -oi -oh
>

With a single input file there's nothing to do.  You need to provide all data 
files (from all of the lambda values) to g_bar.  See my tutorial for details.

-Justin

> swapnil
>
>
> On Wednesday, 13 August 2014 4:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
>
> On 8/13/14, 11:19 AM, Swapnil Kate wrote:
>  > hello,
>  >
>  > I am trying to generate free energy of solvation using g_bar gromacs tool,
>  >
>  > i have carried out all steps given in manual for solvation energy, but when i
> am trying to use g_bar command it shows 'nothing to calculate'.
>  >
>  > what can be the possible errors because i am not getting correct values?
>
>  >
>
> You probably issued the command wrong, but since you haven't provided us with
> your exact command, there's nothing else to suggest.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul

>
>
> ==================================================
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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