[gmx-users] Water models usage info
trevorbrown34 at gmail.com
Mon Jan 10 01:42:51 CET 2011
Thank you for your reply which solved my problem.
I want to add something for all gmx-users. I looked at the force field
folders in share/top in which possible usable water models for each force
field are listed in watermodels.dat files. If you want to use a different
model that is not included in the list, look at the "pdb2gmx" title
at the end of the manual.
On 10/01/2011 2:41 AM, trevor brown wrote:
> Dear friends,
> My run commands are below. It works without any error.
> However if I add -water tip3p at the end of pdg2gmx ... line it causes
> an error (Atomtpe HW not found) at grompp time.
> Could anyone explain the difference?
> pdb2gmx -ignh -f XXX.pdb -o fws.gro -p fws.top
> editconf -f fws.gro -bt dodecahedron -d 1.0
> editconf -f out.gro -o fws_ctr.gro -center 1.7 1.7 1.2
> genbox -cp fws_ctr.gro -cs spc216.gro -o fws_b4em.gro -p fws.top
Not all water models are intended to go with all force fields. G43a1
does not define the HW atom type used for TIP3P water, possibly by
Berk's design :-). I don't remember whether it's reasonable to want to
use TIP3P with the GROMOS forcefields, but presumably SPC water will
work with them.
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