----- Original Message ----- From: ABEL Stephane 175950 <[email protected]> Date: Monday, September 13, 2010 18:06 Subject: [gmx-users] RE : gmx-users Digest, Vol 77, Issue 71 To: [email protected]
> 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 > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
