On 10/15/12 5:45 AM, cuong nguyen wrote:
Dear,
The top file downloaded from PRODRG did not consist of [atomtypes]. Please
tell me how can I add and use this function?
I see no need to change anything about the L-J parameters. Is there some reason
you believe them to be incorrect? If you modify L-J parameters, you're no
longer using Gromos96 43a1. In PRODRG topologies, the charges and charge groups
certainly need changing, but I have never seen a need to hack the L-J parameters.
-Justin
Best regards,
Cuong
On 15 October 2012 16:43, Peter C. Lai <p...@uab.edu> wrote:
Is there no [atomtypes] section in the top file?
On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote:
Thanks for you email.
I already had the .gro and .top files from PRODRG. Now I want to
reproduce
these files following the LJ parameters in a published paper (charge,
sigma
and epsilon values). I can change the charge in the top file, yet I do
not
know how to change sigma and epsilon values.
Best regards,
Cuong
On 15 October 2012 13:57, Peter C. Lai <p...@uab.edu> wrote:
It's hard to understand your question. What do you mean by "reference
parameters"? You said you already obtained a .gro and .top from PRODRG,
which
uses the gromos 43a1 forcefield to derive the parameters, so if you
need
to change the LJ parameters, edit the top file it gave you.
If you want to reproduce the results of a published paper, you should
use
the
forcefield and parameters specified in that paper and contact the
author(s)
if more details are needed.
On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote:
Thank you very much for your email, Justin.
in case I want to use the reference parameters, which force-field and
what
should I do to get the .gro and .top files for this molecule?
Best regards,
Cuong
On 12 October 2012 21:14, Justin Lemkul <jalem...@vt.edu> wrote:
On 10/12/12 8:04 AM, cuong nguyen wrote:
Dear Gromacs Users,
I got the .gro and .top files of 1-octanol downloaded from PRODRG
website.
Please let me know if I can change charge, epsilon and sigma of
the
molecule as written in a paper? and How to do?
Atom types from PRODRG rarely, if ever, need changing. Charges
can be
taken first by chemical homology (group-based approach that makes
Gromos
force fields convenient) and then by calculating the charges
yourself.
For
1-octanol, it should be very straightforward to obtain parameters,
zero
charges on all the C atoms except for the one in the alocohol, then
standard alcohol charges for the C-O-H. Whether or not those
parameters
are sufficiently accurate is up to you to decide, but that's the
approach
one would take with this particular force field.
-Justin
--
==============================**==========
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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(205) 690-0808 |
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