[gmx-users] Fwd: LJ cut-offs
ramezanpour.mohsen at gmail.com
Wed Jan 11 18:46:09 CET 2017
Thanks for your comments. My question was exactly what Dawid clarified.
Sure, I will read those as you suggested.
Dawid, regarding this:
"You need to keep in mind however that each force field was optimized for
given set of cut-offs and
they virtually become part of that FF (just like FF formula and
parameters), so it is strongly recommended
not to change them"
I agree. BUT, using charmm36 in gromacs or other software requires to
change some critical parameters like cut-offs to get a better agreements
with experiments as well as with simulations done with charmm/NAMD.
This is why.
On Wed, Jan 11, 2017 at 5:54 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 1/10/17 10:40 PM, Mohsen Ramezanpour wrote:
>> Dear gromacs users,
>> Please let me know your opinion on the following question:
>> Thanks in advance for your comments
> While that paper (obviously) focuses on CHARMM, there is a vast amount of
> general MD information described in it, as well as cited literature. The
> section on nonbonded interactions probably addresses most of what you want
> to know.
>> ---------- Forwarded message ----------
>> From: Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
>> Date: Thu, Jan 5, 2017 at 5:20 PM
>> Subject: LJ cut-offs
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Dear Gromacs users,
>> Every force field has been parametrized with a specific LJ cut-off which
>> must be the same for simulations using that force field.
>> However, I was wondering if there is any reason why people usually take
>> even numbers (e.g. 8-10, 8-12, 10-12 all with a difference of 2) for LJ
>> cut-offs in force field development?
>> Is there any rule that prohibit the use of 9-10, 9-11, or 11-12 for LJ
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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