[gmx-users] Re: question on pulling 2 groups in afm run

[Emily Walton]

Hi Linchen,

You may want to try adding the line "ngroups=2" to the pull.ppa,  
right under "runtype = afm". It's in the new manual (version 3.3,  
section 6.2.3). Otherwise, I believe the number of groups defaults to  
1, and that's why mdrun gets confused about finding a group_2,  
afm_rate2, etc. - it's only looking for one of each.

I don't promise that will fix your problem, since I don't do much  
with pulling on multiple groups, but it's a good bet on a place to  
start. If that doesn't fix it, post the actual error messages.

-Emily Walton

> Dear gromacs users,
>     I met a problem on pulling 2 groups in a afm pulling run. When  
> mdrun processes input file, error messages such as "unknown left- 
> hand : group_2" appear for group_2, afm_rate2, afm_k2, afm_dir2 and  
> afm_init2. However, pulling one group is OK.
>     My pull.ppa is
>     verbose = yes
>     runtype = afm
>     group_1 = a_TER1
>     group_2 = a_TER2
>     pulldim = N N Y
>     afm_rate1 = 0.01
>     afm_rate2 = 0.01
>     afm_k1    = 1000
>     afm_k2    = 1000
>     afm_dir1  = 0 0 1
>     afm_dir2  = 0 0 1
>     afm_init1 = 13.639 3.264 4.486
>     afm_init2 = 14.221 3.873 2.790
>     The group definition in pull.ndx is
>     [ a_TER1 ]
>        1136
>     [ a_TER2 ]
>        2425
>     Could anyone tell me what's wrong here? Thanks a lot
>     Best
> regards
>
>                                                                        
>                   Linchen Gong
>
>
>
>
>
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