Thank you for your helpful comments. I am totally convinced that I was not using proper force field.
Best, moeed On 28 February 2011 18:12, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Moeed wrote: > >> Dear Justin, >> >> Thank you for your message. My objective is to calculate interaction >> energies between polymer (polyethylene) and hydrocarbon solvent ( also FE >> calculations). I am using rlist of 1.1 nm. >> >> 1- Do I need to increase rlist ( to 1.4 nm) to overcome the error message? >> >> > You need an rlist of sufficient size to provide a neighbor searching > buffer. This is described in the manual and has been discussed on this list > within the last few days. > > > 2- As with the electrostatics treatment in my hydrocarbon system ( only C >> and H) I was >> unsure if I need to include electrostatics potentials (although there >> exist partial charges). >> I digged into the literature and found the following articles containing >> nonpolar polymers >> where vdw is the only nonbonded term in the FF. Thats why I switched that >> term off. I appreciate your comments/idea on this. >> >> >> > You can't make ad hoc changes to force fields. I'd say that all you've > done is create an untested, arbitrarily modified version of OPLS. You > should read the primary literature for the force field (which hopefully > you've already done), and refer to charge assignment and the reasons for > assigning partial charges to hydrophobic groups. In real life, there are > electrostatic terms as part of the interactions between all atoms, including > induced dipoles in hydrophobic groups. Although we can't model these > explicitly with non-polarizable force fields, they still exist. > Fixed-charge force fields attempt to replicate this real-life behavior > (with varied success). > > > http://pubs.acs.org/doi/abs/10.1021/ma9600419 >> >> > This paper did not use OPLS, so its treatment of electrostatics is > irrelevant. > > >> http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TXW-40TY56F-16&_user=458507&_coverDate=11%2F30%2F2000&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1650178009&_rerunOrigin=google&_acct=C000022002&_version=1&_urlVersion=0&_userid=458507&md5=bf0b74cfc76e0dafbadf06396fb63745&searchtype=a< >> http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TXW-40TY56F-16&_user=458507&_coverDate=11%2F30%2F2000&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1650178009&_rerunOrigin=google&_acct=C000022002&_version=1&_urlVersion=0&_userid=458507&md5=bf0b74cfc76e0dafbadf06396fb63745&searchtype=a >> > >> >> > This link did not work, so I cannot comment. > > The point is that you should never make ad hoc changes to force fields. > People spend years (if not decades) creating and refining force field > models that work, and though you may find it convenient to ignore certain > terms, you probably shouldn't be. Any reviewer that critiques a paper that > has such changes should be very, very concerned about improper use of force > fields. > > -Justin > > >> Thanks >> Moeed >> >> >> ================================================ >> >> pbc = xyz >> energygrps = PE HEX >> >> ; Run control >> integrator = md >> dt = 0.002 >> nsteps = 500000 ;5000 >> nstcomm = 100 >> >> ; Output control >> nstenergy = 100 >> nstxout = 100 >> nstvout = 0 >> nstfout = 0 >> nstlog = 1000 >> nstxtcout = 1000 >> >> ; Neighbor searching >> nstlist = 10 >> ns_type = grid >> >> ; Electrostatics/VdW >> ;;;;coulombtype = PME >> vdw-type = Shift >> rcoulomb-switch = 0 >> rvdw-switch = 0.9 ;0 >> >> ; Cut-offs >> rlist = 1.1 >> rcoulomb = 1.1 ;1.0 >> rvdw = 1.0 >> >> ; Temperature coupling >> Tcoupl = v-rescale >> tc-grps = System >> tau_t = 0.1 ;0.1 >> ref_t = 400 ;300 >> >> >> ; Velocity generation >> gen_vel = yes >> gen_temp = 300.0 >> gen_seed = 173529 >> >> ; Bonds >> constraints = all-bonds >> constraint-algorithm = lincs >> >> =================================================== >> >> >> >> >> On 28 February 2011 17:12, Justin A. Lemkul <jalem...@vt.edu <mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Moeed wrote: >> >> Dear experts, >> >> Please kindly comment on this error. Thank you very much. >> >> I am getting the known charge group radii error. (in 4.0.7 >> version with the same settings my simulations run with no error) >> >> ========================== >> NOTE 1 [file md.mdp]: >> The sum of the two largest charge group radii (0.205676) is >> larger than >> rlist (1.100000) - rvdw (1.000000) >> >> There was 1 note >> . . . >> >> turning all bonds into constraints... turning all >> bonds into constraints... >> Largest charge group radii for Van der Waals: 0.103, 0.103 nm >> This run will generate roughly 317 Mb of data >> >> =================================== >> >> This error has been discussed several times on the archive after >> release of 4.5.3. Please note that my charge groups are CH3 and >> CH2 only! . To treat this error I dont know If I need to >> increase rlist (as suggested in the first link below) or use >> maxwarn -1 ( second link). How can I diagnose which one to choose? >> >> >> http://lists.gromacs.org/pipermail/gmx-users/2011-January/057830.html >> >> >> http://lists.gromacs.org/pipermail/gmx-users/2011-January/057980.html >> >> >> In the latter case, the problem was a result of groups being split >> by PBC. This is not your problem. Be careful about taking posts >> out of context. >> >> It's usually better to increase rlist for proper energy >> conservation. You haven't posted your .mdp file (which is usually >> pretty important for understanding what's going on), but I'll assume >> you're using some sort of switch or shift function for either van >> der Waals or Coulombic interactions. In this case, the manual is >> pretty clear about proper use, although you appear to not be using >> any charges at all. How does that make sense? What is your >> objective? Even OPLS hydrophobic moieties should have small partial >> charges across C-H bonds. >> >> -Justin >> >> >> ================================================== >> charge groups of solute: >> >> 1 opls_135 1 EthB C1 1 0 >> 12.011 ; qtot 0 >> 2 opls_140 1 EthB H11 1 0 >> 1.008 ; qtot 0 >> 3 opls_140 1 EthB H12 1 0 >> 1.008 ; qtot 0 >> 4 opls_140 1 EthB H13 1 0 >> 1.008 ; qtot 0 >> 5 opls_136 1 EthB C2 2 0 >> 12.011 ; qtot 0 >> 6 opls_140 1 EthB H21 2 0 >> 1.008 ; qtot 0 >> 7 opls_140 1 EthB H22 2 0 >> 1.008 ; qtot 0 >> 8 opls_136 1 EthB C3 3 0 >> 12.011 ; qtot 0 >> 9 opls_140 1 EthB H31 3 0 >> 1.008 ; qtot 0 >> 10 opls_140 1 EthB H32 3 0 >> 1.008 ; qtot 0 >> 11 opls_136 1 EthB C4 4 0 >> 12.011 ; qtot 0 >> 12 opls_140 1 EthB H41 4 0 >> 1.008 ; qtot 0 >> 13 opls_140 1 EthB H42 4 0 >> 1.008 ; qtot 0 >> >> ================================== >> >> Thanks >> moeed >> >> >> -- ======================================== >> >> 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 >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> Moeed Shahamat >> Graduate Student (Materials Modeling Research Group) >> McGill University- Department of Chemical Engineering >> Montreal, Quebec H3A 2B2, Canada >> Web: >> http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php >> Web:http://mmrg.chemeng.mcgill.ca/ >> >> > -- > ======================================== > > 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 > > ======================================== > -- > 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! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Moeed Shahamat Graduate Student (Materials Modeling Research Group) McGill University- Department of Chemical Engineering Montreal, Quebec H3A 2B2, Canada Web: http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php Web:http://mmrg.chemeng.mcgill.ca/
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