This is a MIME-encapsulated message
--==_08222125209328.ams1.ulsop.ac.uk==_
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Content-Disposition: inline
Dear Amber users,
I am trying to run an MD simulation where the non-bonded interactions of a=
small group of atoms are set to zero, to investigate the steric effect of=
this group. (I can't just cut it off as it's required to tether two other=
bits of the molecule together.) I did this by creating new atom types with=
identical bonding parameters to the atoms they were replacing, but with=
VDW parameters 0.00 0.00, and setting the charges to zero also.
The system minimised fine, giving sensible geometry and energies compared=
to the original system, which also runs unproblematically. The system=
however gives NaN halfway through an MD simulation when two atoms come=
close to each other. Physically, I can't see any reason why the atoms=
shouldn't be able to pass through each other, but possibly there is some=
place in the code where 1/0 is evaluated, or some other reason.
So, is it possible to somehow turn off the VDW/electrostatic evalutions for=
particular atoms or pairs of atoms entirely, without running the risk of=
this behaviour? If anyone has done this sort of thing before and can=
suggest a good approach that would be very useful.=20
Thanks
Dave Evans
London School of Pharmacy
--==_08222125209328.ams1.ulsop.ac.uk==_
Content-Type: text/directory; charset="iso-8859-1"; profile="vcard"; name="david_evans.vcf"
Content-Transfer-Encoding: quoted-printable
Content-Disposition: attachment; filename="david_evans.vcf"
BEGIN:VCARD
VERSION:3.0
PRODID:-//Gordano//NONSGML GMS 9.02.3180//EN
REV:2004-01-22T09:31:19Z
FN:
N:;;;;
EMAIL;TYPE=3DINTERNET:david.evans.ulsop.ac.uk
END:VCARD
--==_08222125209328.ams1.ulsop.ac.uk==_--
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Apr 21 2004 - 09:53:19 PDT
