Hi
I never had to change masses in the nb.itp and I ran lots of simulations
with the amber-Port...Are you sure, that you had no dummies with mass
zero or so?
REgards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
George Abadir wrote:
Hi,
Actually I think that although the .atp file seems to be used, the
masses in the ffamberxxnb.itp file must be changed from the zero values
to the correct ones: when I ran a simulation without changing them I got
infinite velocities and which did nor happen when I changed the masses
to the correct ones.
Thanks,
George
David van der Spoel wrote:
Maik Goette wrote:
David
I think, I should not contradict to one of the developers, but if
your statement is true:
1. Where, in fact, are the masses coming from (the masses in the
amberFF port can only be found in the atp, as far as I know)?
2. Why does GROMACS complain about missing atoms in the atp-file, if
I add a new atom type to the nb-section?
Just out of curiosity...
Hm, no problems contradicting me at least... I presume you're right.
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