[gmx-users] lipid.itp LJ-1,4 values involving water

[Erik Lindahl]

Hi,

They were almost certainly auto-generated from the standard parameters.

Cheers,

Erik

On May 3, 2006, at 8:44 PM, chris.neale at utoronto.ca wrote:

> Does anyone know why lipid.itp contains [pairtypes] LJ-1,4 values  
> including
> lipid atoms and OW or HW? I can understand their inclusion in  
> [nonbond_params],
> but it seems as if this would never be required in [pairtypes].
>
> ***
>
> In case anyone else is trying to merge lipid.itp and OPLSAA, here  
> is what I have
> done. There is no type of guarantee here, just a listing of what  
> appears to be
> working so far for me.
>
> Download lipid.itp and pope.itp (or your lipid) from
> http://moose.bio.ucalgary.ca/ kindly made available for all by Dr.  
> Peter Tieleman.
>
> 1. Added [atomtypes] from lipid.itp to ffoplsaanb.itp -- after  
> changing c6/c12
> to sigma/epsilon. Also added atomtype H from olsa_369 to match H  
> expected by
> pope.itp
>   - sigma   = (c12/c6)^1/6
>   - epsilon = c6/(4*sigma^6)
>
> 2. Added [pairtypes] from lipid.itp to ffoplsaanb.itp -- after  
> changing c6/c12
> to sigma/epsilon. (gives effective fudgeLJ of 0.125). Also changed  
> all reference
> to OW to opls_116 (opls spc water oxygen) and simply removed any  
> with reference
> to HW as it will be zero regardless.
>
> 3. Added [dihedraltypes] from lipid.itp to ffoplsaabon.itp.
>   - Prior to running ensure that the non-RB dihedral does not exist  
> for these
> groups.
>
> 4. make a topology file like this:
>
> #include "ffoplsaa.itp"
> #include "myprotein.itp"
> #include "spc.itp"
> #include "pope.itp"
>
> [ system ]
> system_name
>
> [ molecules ]
> ; Compound        #mols
> Protein             1
> POPE              299
> SOL              8991
>
>
>
>
>
>
>
>
> _______________________________________________
> 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
>