[EMAIL PROTECTED] wrote:
Hi,GMX group and other users:
I am a gromacs(version 3.3) user. I want to do carbon nanotube(CNT) MD.
Months ago, when I ran grompp, she told me that something was wrong.
(see http://www.gromacs.org/pipermail/gmx-users/2006-April/021092.html)
After i got suggestions from GMX group and other users (really thank Bob
who has given me some importent advices!) and checked almost
all of the "Mailing lists" about CNT, i began other ways to generate
my files (.gro .top and so on).
This morning i got the results of my working----ERRORS!
So I type this for help AGAIN.
I will tell what I have done in details, may anyone could give me a hand.
<What i have?>
a "cnt.pdb" and a "cnt.gro" which i write by myself on the base of "cnt.pdb"
You can generate a gro file from pdb by editconf but you don't need it
for this.
The easiest way to get a topology is to use x2top. The errors you showed
are probably due to periodic boundary conditions.
Is your nanotube supposed to be infinitely long? In that case, is the
box size in the pdb file correct?
If it is not supposed to be infinite you need to cap the ends with
hydrogen atoms or something like that.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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