[gmx-users] Problems with umbrella sampling

[Justin A. Lemkul]

Amir Marcovitz wrote:
> Thanks Justin,
>  
> it seems to help, i have another general question that you might help me 
> with:
>  
> should i define the distances for the umbrella sampling run in some file 
> and then run it?(i saw something about  *.ppa file but couldn't find any 
> further instructions in the mannual..)
> will this file apply for the WHAM analysis after the run?
>  

All settings are defined in the .mdp file (see, i.e. pull_start and pull_init). 
  Using .ppa files is obsolete (version 3.x and before).  The WHAM analysis 
later reads these distances from the .tpr files passed to g_wham.

There are many discussions (some quite recent) in the list archive about proper 
settings.  I suggest you have a look at the manual and then go searching.

-Justin

> thanks,
> Amir
> 
> On Mon, Dec 28, 2009 at 6:14 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Amir Marcovitz wrote:
> 
>         Hi,
>          my system is constructed of 2 parallel plates in a box with
>         solvent. each plate is made of 36 atoms which are positively
>         charged on one of them (SRP) and negatively charged on the other
>         plate (SRN).
>          i want to perform a simulation with umbrella sampling between
>         the 2 so i defined the pulling section parameters in the .mdp
>         parameter file as following:
>          ; COM PULLING         ; Pull type: no, umbrella, constraint or
>         constant_force
>         pull                     = umbrella
>         ; Pull geometry: distance, direction, cylinder or position
>         pull_geometry            = distance
>         ; Select components for the pull vector. default: Y Y Y
>         pull_dim                 = Y Y Y
>         ; Cylinder radius for dynamic reaction force groups (nm)
>         pull_r1                  = 1
>         ; Switch from r1 to r0 in case of dynamic reaction force
>         pull_r0                  = 1.5
>         pull_constr_tol          = 1e-06
>         pull_start               = no
>         pull_nstxout             = 10
>         pull_nstfout             = 1
>         ; Number of pull groups
>         pull_ngroups             = 2
>         ; Group name, weight (default all 1), vector, init, rate
>         (nm/ps), kJ/(mol*nm^2)
>         pull_group0              = SRP
>         pull_weights0            = 1
>         pull_pbcatom0            = 0
>         pull_group1              = SRN
>         pull_weights1            = 1
>         pull_pbcatom1            = 0
>         pull_vec1                = 0.0 1.0 0.0
>         pull_init1               = 1.5
>         pull_rate1               = 0
>         pull_k1                  = 1
>         pull_kB1                 = 0
>          when proccesing the file with grompp i get the following error:
>          *Fatal error:
>         Number of weights (1) for pull group 0 'SRP' does not match the
>         number of atoms (36)*
>          is someone recognizing my mistake?
> 
> 
>     Please refer to the manual (manual.gromacs.org
>     <http://manual.gromacs.org/> is quite handy), you will find:
> 
>     "Optional relative weights which are multiplied with the masses of
>     the atoms to give the total weight for the COM. The number should be
>     0, meaning all 1, or the number of atoms in the pull group."
> 
>     I also think your value for pull_ngroup is wrong.  It appears you
>     are pulling SRN with respect to SRP, so you only have one pull
>     group, not two.
> 
>     -Justin
> 
>         does someone has an experience with umbrella sampling in GROMACS?
>          thanks'
>         amir
>         *
>         *
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     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
> 
>     ========================================
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> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================