[gmx-users] Question about DNA simulation

Maik Goette 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
37077 Goettingen
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:
> 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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