[gmx-users] umbrella sampling - gromcas 5.0.4

[CARDELLINI ANNALISA]

Thank you very much Nima!!
Annalisa





On Thu, 5 Mar 2015 02:01:33 +0000 (UTC)
  Nima Soltani <Nima.slt at gmail.com> wrote:
> 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
> 
> 
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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