[gmx-users] Question about DNA simulation
mgoette at mpi-bpc.mpg.de
Tue Jun 19 14:57:50 CEST 2007
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?
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
George Abadir wrote:
> 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.
> David van der Spoel wrote:
>> Maik Goette wrote:
>>> 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.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users