[gmx-users] Use dihedraltype 4 to allow several multiplicity terms

[Justin Lemkul]

On 3/7/13 10:46 AM, Steven Neumann wrote:
> Dear Gmx Users,
>
> I used charmm server to get the parameters for my new molecule -
> alkane. i converted it into the gromacs topology.
> When I try grompp:
>
> WARNING 1 [file ffbonded.itp, line 7948]:
>    Overriding Proper Dih. parameters.
>    Use dihedraltype 4 to allow several multiplicity terms.
>
>    old: 0 0.159787 2 0 0.159787 2
>    new: CG331      CG321      CG321      CG331      9          0.00
>    0.1598288  2
>
>
> WARNING 2 [file ffbonded.itp, line 7949]:
>    Overriding Proper Dih. parameters.
>    Use dihedraltype 4 to allow several multiplicity terms.
>
>    old: 0 0.159829 2 0 0.159829 2
>    new: CG331      CG321      CG321      CG331      9          180.00
>    0.1330512  6
>
> My ffnonbonded.itp corresponding lines:
>
> [ dihedraltypes ]
> ; i	j	k	l	func	phi0	cp	mult
> CG331      CG321      CG321      CG331      9          0.00
> 0.1598288  2
> CG331      CG321      CG321      CG331      9          180.00     0.1330512  6
>
> Can you please explain me this? Shall use 4 instead of 2 or 6 at the
> end of these lines?

No, the last entries are the multiplicity, not the function type (which is the 
fifth entry, under "func").  Unfortunately, I cannot answer why grompp is 
prompting you to use type 4, which according to the manual is for periodic 
improper dihedrals, not proper dihedrals.  Maybe you've added those lines in the 
wrong directive, i.e. with impropers rather than propers?

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================