[gmx-users] charmm to gromacs nonbonded parameters after conversion

[Mark Abraham]

----- Original Message -----
From: ABEL Stephane 175950 <Stephane.ABEL at cea.fr>
Date: Monday, September 13, 2010 2:59
Subject: [gmx-users] charmm to gromacs nonbonded parameters after conversion
To: gmx-users at gromacs.org

> Hi GMX users,
>  
> I would like to perform MD with new developped CHARMM parameters 
> in GROMACS. Since these parameters are new, they are not 
> presents in the ffcharm*.itp files  given in the of 
> charmm27.ff in the latest GMX distribution. So I have already 
> made the conversions for the bonded parameters. In case of the 
> nonbonded parameters, I have added the LJ values for the new 
> atom types at the end of the  NONBONDED section of a 
> "par_all_27_lipid.prm" file downloaded from the CHARMM website. 
> To convert the LJ values in GROMACS format, I used the perl 
> script of M. Abraham :  convert_charmm_to_gromacs.pl 
> (v.1.3) as follow : 
>  
> perl convert_charmm_to_gromacs.pl  par_all27_lipid.prm
>  
> I obtain the ffcharmm.itp and ffcharmmnb.itp files as expected. 
> In the ffcharmmnb.itp the [ atomtypes ] section is present but 
> not the [ pairtypes ] section. Moreover the values in the  
> [ atomtypes ]  are different compared to same file given in 
> latest GMX distrib (see below). Why these differences ?
> ----- My ffcharmmnb.itp file 
> [ atomtypes ]
> ;name mass     charge 
> ptype     c6       c12
> ....
>  CTL1 12.011000   0.0     A -
> 0.001485 -6.588e-06 ; -0.000252 -3.793e-07
>  CTL2 12.011000   0.0     A -
> 0.001978 -4.173e-06 ; -0.000252 -3.793e-07
>  CTL3 12.011000   0.0     A -
> 0.003011 -6.944e-06 ; -0.000252 -3.793e-07
>  CTL5 12.011000   0.0     A -
> 0.003274 -8.007e-06 ; -0.000252 -3.793e-07
>  CEL1 12.011000   0.0     A -
> 0.003035 -8.095e-06
> ....
> ------ GROMACS 4.5.1  ffcharmmnb.itp
> 
> [ atomtypes ]
> ;name at.num mass charge ptype sigma epsilon
> ....
> CTL1 6 12.01100 0.14 A 0.405358916754 0.08368 
> CTL2 6 12.01100 0.05 A 0.358141284692 0.234304
> CTL3 6 12.01100 -0.27 A 0.363486677001 0.326352 
> CTL5 6 12.01100 -0.35 A 0.367050271874 0.33472
> CEL1 6 12.01100 -0.15 A 0.372395664183 0.284512 
> .....
> Thank in advance for your halp 

As the column headings note, the GROMACS 4.5 CHARMM27 uses sigma-epsilon VDW parameters, and my script converted to c6-c12 parameters. As you will see in the appropriate equations in chapter 3 or 4 of the manual, such numbers will be wildly different, but should produce the same energies and forces.

Mark

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