[gmx-users] on force fields
Justin A. Lemkul
jalemkul at vt.edu
Mon Feb 21 03:41:26 CET 2011
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:
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.
> --- On *Wed, 2/16/11, Mark Abraham /<Mark.Abraham at anu.edu.au>/* wrote:
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] on force fields
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> 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).
> -----Inline Attachment Follows-----
> gmx-users mailing list gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users