VMD-L Mailing List
From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Tue Jan 04 2005 - 14:02:50 CST
- Next message: Sabuj Pattanayek: "nvidia quadro, linux_x86, and performance difference w/nvidia drivers 1.0.5336 vs anything newer or older on VMD 1.8.2"
- Previous message: dtp3+_at_pitt.edu: "RE: Re: Re: your mail"
- In reply to: John Stone: "Re: pdb files"
- Next in thread: nordgren_at_sas.upenn.edu: "Re: pdb files"
- Reply: nordgren_at_sas.upenn.edu: "Re: pdb files"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
O>>> "JS" == John Stone <johns_at_ks.uiuc.edu> writes:
JS> ops, I missed seeing Axel's reply. Axel's is a more
JS> complete answer, so I'd suggest starting with his suggestion.
it depends. since i don't usually have residue assignments
in car-parrinello simulations, i tend to forget about them
when you have them, using
'same resid as (name OW and within 20.0 of index 0)'
should be much faster in your case. with car-parrinello MD, you
cannot afford that many atoms, so one tends to get sloppy :-/
[...]
H>>> "VS" == VISWANADHA SRIDHARA <vsrid001_at_odu.edu> writes:
VS> i Axel and John,
VS> One more quick question, Here you mentioned keeping the whole molecule, if
VS> some of its atoms are within the range of the reference point, but what if
VS> it is the other way, if I Want to remove the entire molecule when some of
VS> its atoms are outside the range of the study of reference. Is it possible
VS> just by putting not(same residue as (within 20 of something)), after we
VS> select the pdb file.
ok, that is a little trickier. you have to carefully check the
and/or logic, but something like following (totally untested) might work:
'(same resid as (name OW and within 20.0 of index 0)) and not
same resid as (name HW1 HW2 and not within 20.0 of index 0)'
axel.
VS> Thanks in Advance.
-- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
- Next message: Sabuj Pattanayek: "nvidia quadro, linux_x86, and performance difference w/nvidia drivers 1.0.5336 vs anything newer or older on VMD 1.8.2"
- Previous message: dtp3+_at_pitt.edu: "RE: Re: Re: your mail"
- In reply to: John Stone: "Re: pdb files"
- Next in thread: nordgren_at_sas.upenn.edu: "Re: pdb files"
- Reply: nordgren_at_sas.upenn.edu: "Re: pdb files"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]