[gmx-users] Question about DNA simulation

[George Abadir]

Hi,
    No there were no dummies, and without changing the masses in the 
non-bonded parameters file it would give infinite velocities.
Regards

Maik Goette wrote:

> 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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>
>