[gmx-users] Weird result of WHAM

Netaly Khazanov netalyk at gmail.com
Thu Nov 15 08:41:28 CET 2012

Sorry, I will express  myself more clearly.
1.State A/B  corresponds  to  different conformation states of the protein.
State A is the crystal structure of the protein, suppose to be more stable
than state B (model structure).
And indeed, I've got the expected PMF plot in which clearly can be seen,
that state A is more stable than state B by taking snapshots  from the path
A to B.
In order to check myself, I did the same to the snapshots that were taken
from the trajectory path from the B to A and I've got the opposite results.
( State B is more stable than state A by the same magnitude of delta G!)

Umbrella sampling for 10ns :
; Pull code
pull            = umbrella
pull_geometry   = distance
pull_dim        = Y  Y  Y
pull_start      = yes
pull_ngroups    = 1
pull_group0     = O1G_O2G_O3G_PG_&_ATP
pull_group1     = r_90
pull_init1      = 0
pull_rate1      = 0.0
pull_k1         = 1000      ; kJ mol^-1 nm^-2
pull_nstxout    = 1000      ; every 2 ps
pull_nstfout    = 1000      ; every 2 ps

Wham analysis command:
g_wham_d -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 1000

2. By merging  the data of the both path, I meant that I added tpr files
and pullf files from the path B to A  to the
 files tpr-files.dat/ pullf-files.dat of the path A to B and calculated
WHAM.. I can do it since it is the same reaction coordinates in both cases,
can't I?
The result PMF plot shows that state A is more stable than state B like I
So I really don't know what I am doing wrong while analysing
the snapshots from path B to A.
Any ideas?

On Wed, Nov 14, 2012 at 8:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 11/14/12 8:43 AM, Netaly Khazanov wrote:
>> Dear All,
>> I've performed TMD simulation using NAMD program from the state A to B,
>> and
>> visa versa from the state B to A.
>> Umbrella sampling calculations were done on the snapshots that were  taken
>> from the path ( A to B & B to A) by using Gromacs.
>> Afterwards WHAM analysis was calculated in order to extract PMF plot.
>> However the result of  ΔG of PMF plot  in the case of A to B path was the
>> opposite (for example -10)  than in the case of B to A ( 10). ( I would
>> expect to get the same result in both cases).
> Can you explain in greater detail what states A and B correspond to?  I
> would expect the opposite - the reverse of a process should have the same
> magnitude of deltaG and opposite sign (i.e. ligand binding/unbinding).
>  By merging the data of both paths, WHAM gives result of   ΔG=-10.
>> The result is very not consistence. I'm  probably missing something.
> You'll have to be more explicit about what you're doing, i.e. actual
> commands, input, and output.
> -Justin
> --
> ==============================**==========
> 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>


More information about the gromacs.org_gmx-users mailing list