[gmx-users] question about the format of [atomtypes] in ffnonbond.itp

[Mark Abraham]

----- Original Message -----
From: Baofu Qiao <qiaobf at gmail.com>
Date: Friday, September 10, 2010 18:38
Subject: [gmx-users] question about the format of [atomtypes] in	ffnonbond.itp
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

 
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>  Hi all,
 > 
>  I just realized the the format of defining the atom-name in [atomtypes] section in ffnonbond.ipt in different forcefields are different. such as
>  1. oplsaa.ff/
>  [ atomtypes ]
 > ; name  bond_type    mass    charge   ptype          sigma      epsilon
 >  opls_001   C   6      12.01100     0.500       A    3.75000e-01  4.39320e-01 ; SIG
 > 
>  2. charmm27.ff (similar as amber99.ff and gromos53a6.ff)
>  [ atomtypes ]
 > ;name   at.num  mass    charge  ptype   sigma   epsilon
 > C       6       12.01100        0.51    A       0.356359487256  0.46024
 > 
>  3. Martini FF
>  [ atomtypes ]
 > ; name mass charge ptype c6 c12
 > P5 72.0 0.000 A 0.0 0.0
 > 
>  I wonder how gromacs deals with these difference smartly? And if I want to write my force field files,  what should I pay attention to this difference?




grompp does a bunch of black-magic sscanf manipulation, inferring things from the number of entries on lines and whether they are numbers or whatever. You don't want to know :-)




For design purposes, matching any of them is probably fine. charmm27 looks like a reasonable compromise between information and noise. I can't think of an application for grompp knowing an atomic number, but it can't hurt.




Mark

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