[gmx-users] umbrella sampling - gromcas 5.0.4

[CARDELLINI ANNALISA]

Dear gromacs users,
I am Annalisa and I am using gromacs 5.0.4 (umbrella 
sampling module) to obtain the PMF between two particles 
(UNK1 and UNK2).
I would like to generate the windows configurations by 
restraining the particle "UNK1" and pulling the particle 
"UNK2" away along the x direction.
Now, I have some problems to define the reference group in 
the pull code.

For previous gromacs versions, the .mdp options were very 
clear:
pull_group0     = UNK1 (reference group)
pull_group1     = UNK2 (pulling group)

In gromacs 5.0.4 the notation is different. The pulling 
group is identified by the option :"pull-group1-name" that 
is UNK2 in my case. However, there is not somenthing like 
"pull_group0"  for the reference group.
A new option ("pull-coord1-groups") has been introduced. 
In "pull-coord1-groups", the two groups indices should be 
given.
My question is: which indices? By giving the indices 
corresponding to the index file, I get the following 
error: "Pull group index in pull-coord1-groups out of 
range, should be between 0 and 3".
How can I set the correct COM PULLING options in the mdp 
file?
Thank you!
Annalisa




Annalisa Cardellini, M.Sc.
Ph.D. student

Politecnico di Torino - Energy Department
Corso Duca degli Abruzzi, 24
10129 Turin - ITALY
Tel: +39-011-090-4495
Fax: +39-011-090-4499

E-mail: annalisa.cardellini at polito.it
SMaLL: http://www.polito.it/small