[gmx-users] Question about DNA simulation

[George Abadir]

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.
>