Jones de Andrade wrote:
Hi all.
Well, I'm having a bit of trouble here because the work has decided to
go in the direction of something I've never used before with gromacs:
dummy atoms (or now "virtual sites").
I assume this is not for a protein, in which case pdb2gmx does it for you.
I've got at least three questions in order to use them:
1 - does the virtual sites need to be included in the .gro files in
order to make a simulation run?
Yes.
2 - do I need to include them in the "exclusion list"?
It depends, but usually yes.
3 - do I need to include them in the "atoms" section?
Yes.
Thanks a lot in advance for any help anyone can provide in these
subjects. ;)
Check the mannual too. Chapter 5. An dtopologies for TIP4P, TIP5P etc.
Sincerally yours,
Jones
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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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