[gmx-users] umbrella sampling - gromcas 5.0.4

[Nima Soltani]

CARDELLINI ANNALISA <d021974 at ...> writes:

> 
> 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?
The indices that you should mention at pull-coord1-groups has nothing to do
with the index file
it is indices you use to identify your groups that participate in a given
reaction coordinate 
in your case that you have one reference and one pulling group that are
participating in one reaction coordinate you should have something like that:
.
pull-ngroups = 2
pull-ncoords = 1
pull-coord1-groups = 1 2
pull-group1-name = refgroup
pull-group2-name = pullgroup
.

"pull-coord1-groups = 1 2" section specifies that group 1 and 2 are
participating in reaction coordinate 1 which is the only reaction coordinate, 

I recommend you to see this explanation given by Dr. Justin Lemkul:
http://permalink.gmane.org/gmane.science.biology.gromacs.user/67963

> 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 ...
> SMaLL: http://www.polito.it/small


Best Regards
Nima Soltani
Graduate student
Sharif University of Technology