I went through few papers related to OPLS-AA, but could not find any specific values mentioned for vdw and coulomb intecations.. In one of the papers ".....In most cases, the intermolecular nonbonded interactions were truncated at 11Å based on roughly the center-of-mass separations with quadratic smoothing of the interaction energy to zero over the last 0.5 Å. The cutoff for alkenes and acetals was 13 Å, while for propanol, cyclohexane, 2-methyl-2-propanol, phenol, ethyl methyl sulfide, NMA, DMA, and NMP it was extended to 15 Å....." J. Am. Chem. Soc. 1996, 118, 11225-11236.
So does this cut off refer to coulombic interactions? is it correct if iI use the following parameters for OPLS-AA force field? ----------------------------------------------------------------------------- ;NEIGHBOUR SEARCHING nstlist = 10 ; FREQUENCY WITH WHICH NEIGHBOURLIST IS UPDATED ns_type = grid ; TYPE OF NEIGHBOUR SEARCH GRID OR SIMPLE pbc = xyz ; DIRECTION OF PERIODIC BOUNDARY CONDITIONS USAGE rlist = 1.4 ; CUT-OFF DISTANCE FOR SHORT RANGE NEIGHBOUR LIST ;ELECTROSTATICS coulombtype = PME ; METHOD FOR CALCULATING COULOMIC INTERCATION - PARTICLE MESH EWALD rcoulomb = 1.4 ; CUTOFF DISTANCE FOR ELECTROSTATIC INTERACTIONS epsilon_r = 1 ; RELATIVE DIELECTRIC CONSTANT ;VAN DER WAALS vdwtype = Switch ; METHOD FOR TREATING VANDERWAAL'S FORCES rvdw_switch = 0.9 rvdw = 1.00 ; CUTOFF DISTANCE FOR LJ OR BUCKINGHAM INTERACTIONS -------------------------------------------------------------------------------------------------------------------- Thanks MKS On Sat, Jan 22, 2011 at 6:41 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Kavyashree M wrote: > >> Sir, >> >> Yes sir I am using PME. And one more thing I noticed was, the protein >> has >> 7 disulphide bonds, so when I reduce all the cystine to cysteine or to >> alanine, >> the the sum of charge group radii reduces from 0.31..nm to 0.30..nm and >> also the >> value of this is identical in case of alanine mutation or cysteine >> mutation. >> I finalised on the value of rlist = rcolomb = 1.35nm so as not to take >> risk. >> is that fine? >> >> > > As I said before, read the OPLS paper. 1.35 nm does not sound right. > > -Justin > > Thank you >> M. Kavyashree >> >> >> On Sat, Jan 22, 2011 at 6:26 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Kavyashree M wrote: >> >> Sir, >> >> System is a protein with 123 aa. No modifications were made >> on the pdb file, >> and it was submitted to pdb2gmx by removing all HETATMs, >> retaining only protein >> atoms. topology was created entirely by pdb2gmx and no other >> molecule was introduced. >> >> I will go through the OPLSAA paper, but if I increase rlist >> to 1.4nm without reducing >> rvdw according to "The Origin of Layer Structure Artifacts in >> Simulations of Liquid Water" >> - JCTC, 2006, 2, 1-11, will it not cause orderedwater shell >> during simultion? >> >> >> You're using PME. In the first paragraph of the introduction, it is >> stated that the spurious effect does not occur with PME. >> >> -Justin >> >> >> Thanking you >> M. Kavyashree >> >> >> On Sat, Jan 22, 2011 at 12:27 AM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Kavyashree M wrote: >> >> Sir, >> >> What exactly can be wrong with the topology? As I tried >> with >> >> >> I don't know, what's in your system? Was the topology created >> entirely by pdb2gmx, or have you introduced some other molecules >> that you've parameterized? >> >> >> different PDBs of same structure at higher resolutions >> too, I am >> getting >> almost similar charge group radii, so can you kindly >> elaborate about >> what can go wrong in the topology to get such values? >> >> >> Large charge groups indicate that a fair number of atoms have >> been >> included in the same charge group. Usually only two or three >> atoms >> are in a charge group, rendering them fairly small. With >> PME, the >> effects may not be that large, i.e. >> >> http://lists.gromacs.org/pipermail/gmx-users/2010-November/056219.html, >> but it's still worth investigating what your largest charge >> group is >> that's causing this problem. If the topology is sound and is >> based >> entirely upon standard force field files, it may suffice to >> simply >> increase rlist to 1.4 nm, leaving all the other cutoffs at 1.0, >> which I believe is standard for OPLS (but don't just take my >> word >> for it). >> >> -Justin >> >> >> 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> <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> >> <mailto: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> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- ======================================== >> >> >> 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 >> >> >> > -- > ======================================== > > 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 >
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