[gmx-users] Re: question on pulling 2 groups in afm run
Emily Walton
ewalton at MIT.EDU
Thu May 11 14:36:25 CEST 2006
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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