Thank you Justin, It is good to know i am not alone to not understand. So I will ask to the authors the reason of this discrepancy.
Bye SA 2011/3/28 <gmx-users-requ...@gromacs.org> > ----- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110328/33c5a2e5/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Mon, 28 Mar 2011 07:27:11 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] mathematical expression to obtain the C6 and > C12 LJ terms for the GROMOSXX ff family > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4d90708f.7000...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > sa wrote: > > Thank you Justin for your response > > > > > > I have tried g_sigeps with the OM type LJ values (sigma (nm) = 0.3137 > > and epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol > > 31, 6, 1117) as an example. Unfortunately i can't retrieve the C6 and > > C12 values given for the same in the GROMOS53A6 ffnonbonded.itp. I used > > the following command > > > > I cannot explain this discrepancy. Going back to the actual 53A6 source > (Oostenbrink et al. JCC 2004: 25: 1656-1676), the parameters in > ffnonbonded.itp > are correct with respect to the original force field. The fact that Poger > et > al. claim the parameters are the same does not make sense to me. You may > wish > to contact the authors of that paper directly if you have questions about > reproducing their results. I also find it curious that they list their > values > in sigma/epsilon rather than the conventional C6/C12 used by Gromos96 force > fields. > > -Justin > > > g_sigeps_mpi -sig 0.3137 -eps 1.2231 and obtained the output > > > > c6 = 4.66239e-03, c12 = 4.44320e-06 > > sigma = 0.31370, epsilon = 1.22310 > > Van der Waals minimum at 0.352116, V = -1.2231 > > > > Fit of Lennard Jones (12-6) to Buckingham: > > A = 199065, B = 34.0796, C = 0.00466239 > > > > Back Off! I just backed up potje.xvg to ./#potje.xvg.8# > > > > gcq#342: "Ich war schwanger, mir gings zum kotzen" (Nina Hagen) > > > > > > Did I miss something ? > > > > Thank you again for your help > > > > SA > > > > > > > > > > sa wrote: > > > Dear All, > > > > > > I would like to compute the C6 and C12 LJ terms for the GROMOS > > 53A6 ff > > > for a new atom type and incorporate them in my ffnonbonded.itp. > Does > > > anybody know the mathematical expressions used to obtain these > terms > > > from a sigma (nm) and an epsilon (kj/mol) values manually. > > > > > > > g_sigeps can do this for you. Otherwise, you can convert between > > the two common > > forms of the Lennard-Jones equation. > > > > -Justin > > > > > Thank you for your help. > > > > > > SA > > > > > > > -- > > ======================================== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > > > > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 4 > Date: Mon, 28 Mar 2011 14:07:31 +0200 > From: sa <sagmx.m...@gmail.com> > Subject: [gmx-users] Re: mathematical expression to obtain the C6 and > C12 LJ terms for the GROMOSXX ff family > To: gmx-users@gromacs.org > Message-ID: > <AANLkTimWtTB4V_=ngpbvp9ga4zrnaroxnh-rqt-pr...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Sorry I forget to say in my previous mail that the values obtained by > g_sigeps_mpi are not similar to the values given in > the GROMOS53A6 ffnonbonded.itp for the OM atom. > > OM 8 0.000 0.000 A 0.0022619536 7.4149321e-07 > > So your advices are welcome. > > SA > > > 2011/3/28 sa <sagmx.m...@gmail.com> > > > Thank you Justin for your response > >> > > > > I have tried g_sigeps with the OM type LJ values (sigma (nm) = 0.3137 and > > epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol 31, > 6, > > 1117) as an example. Unfortunately i can't retrieve the C6 and C12 > values > > given for the same in the GROMOS53A6 ffnonbonded.itp. I used the > following > > command > > > > g_sigeps_mpi -sig 0.3137 -eps 1.2231 and obtained the output > > > > c6 = 4.66239e-03, c12 = 4.44320e-06 > > sigma = 0.31370, epsilon = 1.22310 > > Van der Waals minimum at 0.352116, V = -1.2231 > > > > Fit of Lennard Jones (12-6) to Buckingham: > > A = 199065, B = 34.0796, C = 0.00466239 > > > > Back Off! I just backed up potje.xvg to ./#potje.xvg.8# > > > > gcq#342: "Ich war schwanger, mir gings zum kotzen" (Nina Hagen) > > > > > > Did I miss something ? > > > > Thank you again for your help > > > > SA > > > > > > > > > >> sa wrote: > >> > Dear All, > >> > > >> > I would like to compute the C6 and C12 LJ terms for the GROMOS 53A6 ff > >> > for a new atom type and incorporate them in my ffnonbonded.itp. Does > >> > anybody know the mathematical expressions used to obtain these terms > >> > from a sigma (nm) and an epsilon (kj/mol) values manually. > >> > > >> > >> g_sigeps can do this for you. Otherwise, you can convert between the > two > >> common > >> forms of the Lennard-Jones equation. > >> > >> -Justin > >> > >> > Thank you for your help. > >> > > >> > SA > >> > > >> > >> -- > >> ======================================== > >> > >> Justin A. Lemkul > >> Ph.D. Candidate > >> ICTAS Doctoral Scholar > >> MILES-IGERT Trainee > >> Department of Biochemistry > >> Virginia Tech > >> Blacksburg, VA > >> jalemkul[at]vt.edu | (540) 231-9080 > >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >> > >> ======================================== > >> > >> > >> > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110328/6efb602a/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Mon, 28 Mar 2011 12:37:51 +0100 > From: Andr? Ferreira <a...@eq.uc.pt> > Subject: [gmx-users] No DD grid found > To: gmx-users@gromacs.org > Message-ID: <4d90730f.7060...@eq.uc.pt> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear all, > > I am having some problems with some molecules that I am currently > simulating. I got simulation box that is constituted by 100 oligomer > molecules (190 atoms each), in a cubic box with 7 nm side (50K). Since > the molecule is quite long I am using a rcoulomb of 2.8 nm and rvdw of > 3.4 nm. When I try to perform the simulation mdrun can't find DD grid > for more than 48 cores, which is a huge handicap. This is the first time > that I am working with longer molecules, and I never had this problem. > > Really appreciate the help, > André > > > ------------------------------ > > Message: 6 > Date: Mon, 28 Mar 2011 23:13:04 +1100 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] converting L to D amino acid in the CHARMM > force field in GROMACS where to alter dihedral > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4d907b50.1040...@anu.edu.au> > Content-Type: text/plain; charset="iso-8859-1" > > On 28/03/2011 8:45 PM, maria goranovic wrote: > > That would mean that a new residue type will not be required? I just > > need the correct input D-coordinates? > > Try it, before asking about it :-) I said "I suspect you do not need to > change anything about the topology", but I haven't actually done > anything like this ever. Topologies and code shouldn't care about > chirality, so you shouldn't need to do anything other than input the > configuration you want. > > Mark > > > On Sat, Mar 26, 2011 at 2:02 AM, Mark Abraham <mark.abra...@anu.edu.au > > <mailto:mark.abra...@anu.edu.au>> wrote: > > > > On 26/03/2011 2:27 AM, maria goranovic wrote: > >> Yes, that would be the correct way to do this. I was hoping to > >> take a shorter route, and just modifying a couple of dihedrals in > >> the topology files output by pdb2gmx without having to make a new > >> residue. Is that not possible at all ? > > > > Unlike (say) AMBER's leap, pdb2gmx doesn't generate coordinates in > > a general sense. It generates a topology that matches given > > coordinates, fixing a few details as directed. It will fill > > valences with hydrogen atoms, generate terminal groups, organize > > disulfides, and choose protonation states of titratable residues, > > but it won't change geometries in the way you seem to want. > > > > Neither does anything in the .top/.itp files stipulate the > > chirality of any center (in all-atom models). Various dihedral > > angles change sign with chirality, but the dihedral functions are > > all symmetric about the y-axis (i.e. even). So I suspect you do > > not need to change anything about the topology. Just use a > > molecule builder to change the chirality of the relevant center in > > the input file to pdb2gmx. > > > > Mark > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110328/cb02fda7/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 83, Issue 196 > ****************************************** >
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