[gmx-users] Simulation in octanol as solvent

[Mark Abraham]

> Dear All
>  I have added octanolas solvent...but now my problem is that if i take the
> itp file as available on the gromacs site (which is in ffoplsaa) there
> are too many warnings related to bond types and if i get an itp generated
> through prodrg then it excludes the aliphatic hydrogens, while my gro
> file has all hydrogens and hence thereafter the coordinates donot
> match....
>  What should i do??

Start from the beginning. If you don't know already whether you want an
simulation in octanol using explicit aliphatic hydrogen or united atoms
then you haven't thought enough about your problem to be allowed anywhere
near a computer. Consider the pros and cons. Find a parametrization of
octanol that is consistent with your choice. Build a topology by hand if
you need to... start small with methanol and get that working and extend
to octanol. Don't try to run before you know how to walk! :-)

Your approach is a bit like a house builder asking how many bedrooms the
owner wants after they've laid the foundations.

>  Should i remove all hydrogens from the octanol gro file...and if yes is
> there any command to do so...as its very tedious to remove all hydrogens
> from 512 molecules...

As Erik said, grep is indeed your friend here.

Mark