Re: [gmx-users] RE : gmx-users Digest, Vol 77, Issue 71

[Mark Abraham]

----- Original Message -----
From: ABEL Stephane 175950 <Stephane.ABEL at cea.fr>
Date: Monday, September 13, 2010 18:06
Subject: [gmx-users] RE : gmx-users Digest, Vol 77, Issue 71
To: gmx-users at gromacs.org

> Thank you Mark for your response
>  
> If understand well, I should only to copy these additional the 
> values in the [atomtypes] section of the ffcharmmnb.itp file 
> without others modifications/corrections. It is correct ?

No, the two styles will not co-operate, because the kind of parameters are fixed by the combination rule in force. You'll have to convert something by hand.

Mark

> > 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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