Thank you all for helping me. I will surely try the ffamber ports
available.
Regards,
monika
Yang Ye wrote:
Please don't use the OPLS NA forcefield. It is largely based on AMBER
(OPLS takes different approach in parameterization, so you know that
direct migration is so correct) and not verifi
I would also suggest amber force field ports. I managed to run a
simulation with Amber ff 99
and TIP3P water model in Gromacs.
Good luck,
Anna
On 10/2/07, Monika Sharma <[EMAIL PROTECTED]> wrote:
> Dear All,
> I want to start nucleic acid simulations. I am using gromacs3.3.1. But I
> could not fi
Please don't use the OPLS NA forcefield. It is largely based on AMBER
(OPLS takes different approach in parameterization, so you know that
direct migration is so correct) and not verified. I had some
communications with that group on this issue. It has some teaching value
on making topology of
Hi,
On the gromacs webpage in user contributions->topologies you have (at
least) 2 forcefields do download that allow you to simulate NA. The first
is OPLS NA records from rnp-group
(http://rnp-group.genebee.msu.su/3d/oplsa_ff.html). It is for gromacs
3.2.1, so minor manual adjustments for 3.3.
the amber port from eric j sorin.
On 10/2/2007 6:44 PM, Monika Sharma wrote:
Dear All,
I want to start nucleic acid simulations. I am using gromacs3.3.1. But
I could not find any mention of Nucleic Acids in any of the
force-field provided by gromacs distro. So does it mean that one _can
not_
Dear All,
I want to start nucleic acid simulations. I am using gromacs3.3.1. But I
could not find any mention of Nucleic Acids in any of the force-field
provided by gromacs distro. So does it mean that one _can not_ simulate
nucleic acids with gromacs. Has anyone tried? And if someone can guide
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