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? 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. http://pubs.acs.org/doi/abs/10.1021/ma9600419 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 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> 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 | (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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