He, Yang wrote:
HI Justin,
Thank you for your reply. I wonder what you mean by saying that I can specify a
custom index group as your group
to be frozen. Can you give me a example about this ?
Chapter 3 of the manual, the make_ndx man page, manual sections 8.1 and D.73 all
provide relevant information.
Also:
http://wiki.gromacs.org/index.php/Index_File
-Justin
Thank you very much.
Yang
________________________________________
From: [email protected] [[email protected]] On Behalf
Of Justin A. Lemkul [[email protected]]
Sent: Saturday, April 18, 2009 11:59 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] restrict two atoms in a group using freezegrps
He, Yang wrote:
HI all users,
I have tried a simple case with two atoms using [position_restraints] but
always it shows the same error :
Segmentation fault (core dumped)
But after I don't use the position_restraints for one atom and then I can run
the case smoothly. It seems that the gromacs doesn't recognize this
[position_restraints];
That may just indicate instability due to the restraints themselves; i.e.,
fixing atomic positions leads to a crash.
Then, I tried the freezegrps but it seems to restrict a whole group. Here, I
wonder whether I can just use this method to restrict several atoms in a whole
group and how to do that.
Like any other Gromacs tool, you can specify a custom index group as your group
to be frozen.
-Justin
Thank you for your any suggestions.
Yang
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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