On 1/21/13 11:00 AM, Mehdi Bagherpour wrote:
hello justin
I used *make_ndx -f md.tpr:
0 System : 35194 atoms
1 DNA : 1012 atoms
2 MG : 4 atoms
3 CL : 29 atoms
4 K : 51 atoms
5 Water : 34098 atoms
6 SOL : 34098 atoms
7 non-Water : 1096 atoms
8 Other : 4 atoms
9 MG : 4 atoms
10 CL : 29 atoms
11 K : 51 atoms
12 Ion : 80 atoms
13 MG : 4 atoms
14 CL : 29 atoms
15 K : 51 atoms
16 Water_and_ions : 34178 atoms
nr : group ! 'name' nr name 'splitch' nr Enter: list groups
'a': atom & 'del' nr 'splitres' nr 'l': list residues
't': atom type | 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
> 1
Copied index group 1 'DNA'
17 DNA : 1012 atoms*
then I used from bellow command:
*trjconv -s md.tpr -f md.xtc -n index.ndx -o md_1.xtc -center*
and then:
*trjconv -s md.tpr -f md_1.xtc -n index.ndx -o md.pdb -pbc mol -ur compact*
but problem is not fixed.
Because you're not doing anything productive. You're just copying an existing
group that has already been demonstrated to be ineffective.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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