[gmx-users] Problems with umbrella sampling

[Justin A. Lemkul]

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 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
> *
> *
> 

-- 
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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

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