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

[Linchen Gong]

Hello Emily,

    Thanks a lot for your help. After Spercifying ngroups, mdrun works without error. I should download a new version of manual right now. :-)


                                                                            Linchen Gong
	

>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
>>
>>
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>
>>
>> End of gmx-users Digest, Vol 25, Issue 40
>> *****************************************
>
>_______________________________________________
>gmx-users mailing list    gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>