[gmx-users] Simulating a particle surface for interaction

[Muhammad Naqvi]

Nice! Thank you!

> Muhammad Naqvi wrote:
> > Hi all,
> > Wonderful community here! FAQs andManuals on one side, nothing beats 
> the advice of experts. Whoever started this forum, thank you. I am 
> learning a lot.
> > 
> > I have a question of my own. I am trying to see the interaction of 
> certain surfactants and co-surfactants at a hydrophobic interface. To 
> that end I have made a gro and top file using the element carbon, 
> minimizing its box size to approximately its atomic radius 0.1nm by 
> editconf, concatenating it by genconf 100 times in x and y directions 
> but only once in z, giving 10000 carbon atoms. This generates a very 
> nice surface. Then I follow up with editconf again to increase the 
> size of the configuration file in the z direction to 10nm as well. So 
> the end result is a 10x10x10nm box with a hydrophobic carbon wall on 
> one side of the box. The wall's integrity is maintained using position 
> restraints of a point for each carbon. To check the correctness of 
> this procedure, I performed a minimization, however, during 
> preprocessing using grompp a fatal error occurred:
> >  
> > Last line read:
> > '[ molecules ]'
> > Invalid order for directive molecules
> > 
> > I would like to inquire as to what this error is and how to avoid 
> it. Just to verify if the manually produced topology or the 
> configuration files were correct, I processed a benzene ring through 
> the same procedure, ending up with the same error. Here is the 
> topology file:
> > 
> > 
> > #include "ffgmx.itp"
> > 
> > [ moleculetype ]
> > ; Name nrexcl
> > carbon      3
> > 
> > [ atoms ]
> > ;   nr      type  resnr resid  atom  cgnr   charge     mass
> >      1       C     1  carbon     CAN     1    0.000  12.0350
> > 
> > [ position restraints ]
> > 1 1 1000 1000 1000 ; restrain every carbon atom to a point
> > 
> > [ molecules ]
> > carbon 10000
> > 
> > Any help would be highly appreciated. 
> > 
> 
> See the manual, Table 5.3 - you're missing the mandatory [system] 
> directive.  If 
> you get an "invalid order" error, either something is out of order or 
> missing.
> 
> -Justin
> 
> > Cheers,
> > Ali
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 
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> End of gmx-users Digest, Vol 70, Issue 41
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