Please be sure to keep the discussion on the gmx-users list and not my personal
inbox.
On 5/5/12 12:27 AM, Shima Arasteh wrote:
You are right.
Corresponding to the articles related to my project, CHARMM27 is often applied.
I don't have any idea about CHARMM36,because I don't know it at all. And I have
not seen it in force field options in running pdb2gmx. Why?
CHARMM36 is a user contribution that was uploaded after the last Gromacs release
and thus was not included. It may be at some point in the future, but for now
you can get it from the user contributions page of the Downloads section of
gromacs.org.
-Justin
Thanks,
Shima
--------------------------------------------------------------------------------
*From:* Justin A. Lemkul <[email protected]>
*To:* Shima Arasteh <[email protected]>; Discussion list for GROMACS
users <[email protected]>
*Sent:* Friday, May 4, 2012 8:50 PM
*Subject:* Re: [gmx-users] choose a force field
On 5/4/12 10:22 AM, Shima Arasteh wrote:
> Dear gmx users,
> Why CHARMM27 is a suitable force field for studying ion channels in membrane?
It describes both protein and lipids quite well, though from what I understand
about CHARMM36, it is probably an even better choice.
> How can I choose the best force field in this field?
>
By doing lots of reading - published articles doing similar things, analysis of
force fields (strengths and weaknesses), etc. A few hours of reading and
thinking will save you weeks or months of wasted time if you find out after
doing your work that a different choice should have been made.
-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> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
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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