Mr Bernard Ramos wrote:
Thanks for the reply on my first querry. I have another one. If I add
a NEW atom type in *.atp file, will Gromacs automatically recognize this
atom type?
Theoretically, yes, provided that you supply any corresponding parameters in,
e.g., ffnonbonded.itp and ffbonded.itp. However, there is an unresolved bug
related to atomtype assignment that may be relevant:
http://redmine.gromacs.org/issues/618
It seems to me that any alterations to the .atp file cause things to break down,
so do not be surprised if there are problems.
-Justin
Thanks.
--- On *Wed, 2/16/11, Mark Abraham /<[email protected]>/* wrote:
From: Mark Abraham <[email protected]>
Subject: Re: [gmx-users] on force fields
To: "Discussion list for GROMACS users" <[email protected]>
Date: Wednesday, February 16, 2011, 1:53 PM
On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote:
Hi everyone!
I need to update the gromos force field 53A6 with the new force
field 53ACARBO (JCC 10 NOV 2010).
1. I will have to change the parameter values in the file
ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are these
the only files that I need to update if I need to switch to a new
force field?
You should make a copy of the whole force field directory into your
working directory, rename the new directory suitably, make a
suitable change to forcefield.doc, and then edit .itp files
suitably. This means you're leaving your reference version untouched
and can edit locally to your heart's content, and can be sure you're
selecting the right force field with pdb2gmx and/or in your .top file.
2. The new force field 53ACARBO has a new gromos functional form
for select torsional potentials. How to I go over implementing
this in gromos?
Preferably as a sum of existing functional forms. Or use tabulated
bonded interactions (see manual and wiki).
Mark
-----Inline Attachment Follows-----
--
gmx-users mailing list [email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<http://us.mc527.mail.yahoo.com/mc/[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
