Shima Arasteh wrote:
Dear Justin,
ok. But I have to regenerate a job done sometime ago, that's why I have
to use this ff. Am I supposed to use the seventeenth option?
Yes, option 17 is the Gromos87-derived united atom force field that was once
called "ffgmx."
-Justin
Cheers,
Shima
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Sent:* Thursday, April 12, 2012 9:07 PM
*Subject:* Re: [gmx-users] Gromos87
Marzinek, Jan wrote:
>
>
> ------------------------------------------------------------------------
> *From:* Shima Arasteh [shima_arasteh2...@yahoo.com
<mailto:shima_arasteh2...@yahoo.com>]
> *Sent:* Thursday, April 12, 2012 4:53 PM
> *To:* Marzinek, Jan
> *Subject:* Re: [gmx-users] Gromos87
>
> Dear Jan,
> I downloaded the file and put it in my working space but does not
appear in my force filed selections? How come?
> What's wrong with it?
>
> Cheers,
> Shima
> You should have downloaded not a single file but the whole force
field which is a folder and the copy it to the directory you working in.
As Felix mentioned it could be number:
> 17: [DEPRECATED] Gromacs force field (see manual)
> so you do not have to download it. Ensure this is a version you need.
>
And please heed the warnings in the manual. This force field is derived
from Gromos87 but many of its contents are not well documented. There
are far better force field that one can (and should) use.
-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
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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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