I am CC'ing this message to the gmx-users list; please continue any future
discussion there. I hadn't realized it was initially posted to gmx-developers,
which is the wrong forum for such questions. Comments inline below.
Emanuel Birru wrote:
Hi Jestin,
Thanks for your advise. Just to make sure that whether I understand you
well or not,
Are you suggesting me to put additional constraints on the topology as
below
[ settles ]
; OW funct doh dhh
1 1 0.1 0.16330
1 1 0.1 0.16330
1 1 0.1 0.16330
Which supposed to represent O-H and H-H in addition to the original O-W?
Yes, but what you've posted is wrong. You need a [constraints] directive that
does indeed replace the effect of [settles]. What you've posted above does not
accomplish that goal and will result in the same fatal error.
-Justin
Thanks,
Emanuel
-----Original Message-----
From: gmx-developers-boun...@gromacs.org
[mailto:gmx-developers-boun...@gromacs.org] On Behalf Of Justin A.
Lemkul
Sent: Friday, 15 October 2010 12:11 PM
To: Discussion list for GROMACS development
Subject: Re: [gmx-developers] More than one settle type
Emanuel Birru wrote:
Hi,
I am about to calculate partition coefficient of a water molecule
using
gromacs 4.0.7 . To do the calculation I used spc water model as a
solvent and as a solute, I just changed the solute's residue name and
use the same itp file as the spc.itp of gromacs with the name sol.itp.
I
can manage to put them in a box as a solute and solvent, but the
problem
arise when I start doing minimization. I tried to minimised using
L-BFGS
and steep. The error message that I got is the following
"Fatal error:
More than one settle type.
Suggestion: change the least use settle constraints into 3 normal
constraints."
You can get the minimization mdp (em1 and em2) files and my solute itp
file (sol) at the following link.
http://hydra.pharm.monash.edu.au/md_project/em1.txt
http://hydra.pharm.monash.edu.au/md_project/em2.txt
http://hydra.pharm.monash.edu.au/md_project/sol.txt
Could any one suggest a solution please.
There are solutions in the list archive and in the error message itself.
You
cannot have two separate blocks of molecules (water) that use SETTLE.
Use an
equivalent [constraints] directive to mimic the effects of SETTLE,
defining two
O-H constraints and an H-H constraint.
-Justin
Cheers,
Emanuel
--
========================================
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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