sreelakshmi ramesh wrote:
Do u mean to say that all the force fields available in gromacs are
default to be used only for LJ potential.
Yes. That's why they all have their [defaults] directives set to use LJ.
-Justin
On Wed, Dec 22, 2010 at 9:32 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
sreelakshmi ramesh wrote:
Dear justin,
I am sorry the file is ffG43a1nb.itp.It
<http://ffG43a1nb.itp.It> <http://ffG43a1nb.itp.It> was a typing
mistake.
The points I raised before still stand:
1. You're not using 43A1, you're using ffgmx, according to that
message from grompp.
2. You can't make a simple change to any of the force fields
included in Gromacs to magically convert them into using Buckingham
potentials. None of them were designed to do that. You'll have to
basically re-write the entirety of the ff*nb.itp file, and then
validate that such a force field model is even valid, because none
of them were parameterized to be.
-Justin
On Wed, Dec 22, 2010 at 9:26 AM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Justin A. Lemkul wrote:
sreelakshmi ramesh wrote:
I am using gromos force field fotr my work and This force
field's files come filled
with LJ functions and now if i want to work with
buckingham potential i changed in default section of
force
field ffG34a21.itp file but it gives me the follwing
errors
ERROR 77 [file ffgmxnb.itp, line 144]:
Trying to add LJ (SR) while the default nonbond type is
Buck.ham (SR)
I should also add that if you think you're using Gromos96
(although
from "ffG34a21.itp" it's not at all clear to me that you're using
any legitimate form of it - 43A1? 43A2? something else?), you're
not. The "ffgmx" force field is a modified form of Gromos87
that is
antiquated and should not be used for new simulations, as
described
in detail in the manual.
-Justin
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
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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