Hello again Still trying to get this carbonate forcefield to work with gromacs. I now know that the tables and so on are being read in correctly as I can get gromacs to reproduce the energies that I get for the various terms when I calculate them by hand/with a separate program. There is stilla a problem with the charge groups however. As when I attempt to split up the atoms in the water molecule the simulation fails. Again checking that I am doing this correctly I would replace:
; at type res nr res name at name cg nr charge mass 1 amber99_61 1 SOL OW 1 0 16.00000 2 amber99_60 1 SOL HW2 1 0.52422 1.00800 3 amber99_60 1 SOL HW3 1 0.52422 1.00800 4 MW 1 SOL MW4 1 -1.04844 0.00000 with ; at type res nr res name at name cg nr charge mass 1 amber99_61 1 SOL OW 1 0 16.00000 2 amber99_60 1 SOL HW2 2 0.52422 1.00800 3 amber99_60 1 SOL HW3 3 0.52422 1.00800 4 MW 1 SOL MW4 4 -1.04844 0.00000 The problem I get (even if I just run water without any carbonate/tabulated potentials) if I do the above is that the settles algorithm fails. I'm obviously missing something fundamental - I'm not even sure that cg nr stands for the charge group. Any help would be greatly appreciated. Gareth On Thu, Mar 25, 2010 at 11:07 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 26/03/2010 7:03 AM, Gareth Tribello wrote: > >> Hello again >> >> I have tried to do as you suggest and use tables but I have a new >> problem. First let me describe my process and then you can let me know >> if there is anything wrong in the stages: >> >> OK so first you include the following directives into the mdp file: >> >> coulombtype = pme (or whatever sort of coulomb interaction you are >> using) >> vdw-type = user >> >> energygrps = Ca CCA OCA OW HW >> energygrp_table = Ca OCA Ca CCA OCA OCA OCA OW OCA HW >> >> Gromacs is then (at some stage) going to look for a series of files called >> >> table.xvg - which is the default 6-12 Lennard Jones that will be used >> for most of the atoms >> table_Ca_OCA.xvg - which are the Buckingham interactions between your >> various atom types. >> table_Ca_CCA.xvg >> table_OCA_OCA.xvg >> table_OCA_OW.xvg >> table_OCA_HW.xvg >> >> These files have the format (and contents) described in section 6.7 of >> the manual. Finally, you define the various energy groups Ca, OCA and >> so on in your index.ndx file. >> >> The problem is that grompp gives me the following error: >> >> "atoms 1 and 2 in charge group 1 of molecule type 'SOL' are in different >> energy groups" >> >> (incidentally these atoms 1 and 2 are OW and HW) >> >> Does this mean that I cannot use different tabulated potentials for >> different atoms in a molecules? By which I mean that I can't use >> different tabulated potentials for the OW Ca and HW Ca interactions for >> example? >> > > Charge groups are the fundamental unit GROMACS uses in constructing a > simulation. Energy groups are the next "higher" layer in the data > structures, and these must be sets of whole charge groups. With some > electrostatics models, looping over charge groups whose charge is preferably > an integer is essential for modelling correct behaviour. GROMACS does a > complex sorting of all the interactions between charge groups into lists > that allow it to iterate over charge groups and energy groups. A user table > then gets applied to a whole intra- or inter- energy-group loop. Thus your > attempt violates this precondition. > > However, PME does not require the use of charge groups for accurate > results, since all inter-atomic electrostatic interactions get treated, > regardless of distance. So you could decompose your water molecules into two > charge groups, O and Hs. (Caveat, a near-brokenly bad PME approximation > might get a little worse with arbitrary charge groups) > > > Final question, as its not clear to me from the manual, if you use a >> tabulated potential for Lennard Jones and you use mix type 2 (so are you >> are providing epsilon and sigma in the input rather than A and B) does >> gromacs still know that it has to manipulate the input parameters in >> order to get the coefficients of the (tabulated) g(r) and h(r) >> dispersion and repulsion functions (I mean the g(r) and h(r) defined in >> section 6.7 of the manual here)? At the same time does it also know not >> to do anything to the parameters you input for the (tabulated) >> buckingham potentials (as for a buckingham you are providing A and C)? >> > > I expect the point of the tables is that GROMACS just uses them per > equation 6.23. Thus I'd expect C6 and C12 in that equation to be constructed > according to whatever combination rule is in force. If you've specified them > explicitly in the topology (see chapter 5), then they will not be > constructed. > > You should be very careful to test your assumptions and deductions about > how all this machinery is working. Do take the time to set up a tabulated > version of a quick non-tabulated calculation to at least make sure you've > done the simple things right! To test the function of eq 6.23, do a > non-table constructed-parameter calculation, a non-table > topology-specified-parameter calculation, a table constructed-parameter > calculation, etc. to be sure you understand what is going on - and that the > code works right! Please consider contributing any insights to a wiki page > on the GROMACS webpage. > > Before you go to all this work please consider my advice of last email. > Unless you have an existing reason to expect some ad-hoc combination of > different interaction functions to work well together, you may find that > your best possible result is a correctly-functioning random number > generator. > > Mark > > On Wed, Mar 24, 2010 at 2:25 AM, Mark Abraham <mark.abra...@anu.edu.au >> <mailto:mark.abra...@anu.edu.au>> wrote: >> >> >> >> ----- Original Message ----- >> From: Matthew Watkins <matthew.watk...@ucl.ac.uk >> <mailto:matthew.watk...@ucl.ac.uk>> >> Date: Wednesday, March 24, 2010 2:59 >> Subject: Re: [gmx-users] Using lennard jones and buckingham terms >> simultaneously >> To: Discussion list for GROMACS users <gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org>> >> >> > Hi Gareth, >> > >> > as Vitaly suggested tabulated potentials seem to be the only way >> > to go, it took me a while to get up to speed on the Gromacs way >> > of doing this, so get in touch if you wish. >> > >> > The tables for buck potentials need to include the standard 1/r6 >> > term whilst what would be the 1/r12 term needs to contain exp(- >> > Bx.rho), the C6 and C12 coefficients can then be put in a >> > standard nonbonded section. You'll need a separated table >> > for each pair of interactions that interact with buckingham >> > potential. Each pair must be an energy group as well. >> > >> > If there is a simpler method I'd love to hear it. >> >> There's probably not a simpler method because it's not a widely-used >> procedure. It shouldn't be used at all unless you have established >> that the combination of functional forms is effective... >> >> Mark >> -- >> 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/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/mailing_lists/users.php >> >> >> -- > 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/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/mailing_lists/users.php >
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