[gmx-users] Angle parameters in Amber port and in Gromacs

Erik Lindahl lindahl at cbr.su.se
Sun Jun 17 14:01:48 CEST 2007


If you convert the unit to kcal/mol you'll find that both potentials  
are likely coarse approximations - roughly 120 degrees equilibrium  
angle, and roughly 70kcal/mol for the force constant.



On Jun 16, 2007, at 6:55 AM, Mark Abraham wrote:

>> Hi,
>>      While performing simulations of urea in water using the AMBER  
>> port
>> for GROMACS, I noticed that the harmonic angle potential  
>> parameters in
>> AMBER99 port (in ffamber99bon.itp) for the angle HNH
>> (hydrogen-nitrogen-hydrogen) are (120,292.88), which are exactly the
>> same parameters used by GROMACS but for the angle CNH
>> (carbon-nitrogen-hydrogen) in the urea.itp file in the /top folder!
>> I was just wondering if the values in AMBER port are correct or if  
>> there
>> is any possibility that the line with these parameters was written in
>> the wrong place in the ffamber99bon.itp .
> Don't know, but if you read the paper that describes the  
> development of
> these parameters, you'd find out.
> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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 mailing list