[gmx-users] gen-pairs, nrexcl and [ pairs ] in itp files
jon.kapla at mmk.su.se
Tue May 13 08:47:19 CEST 2014
On 2014-05-12 15:44, Hardy, Adam wrote:
> Bogdan, I had found that a little while ago but was unable to find again so thankyou for pointing me to it again and writing it in the first place.
> Jon, I hadn't found those file previously and they are consistent with what I have come up with independently so I guess that is a good sign. Out of interest do you use GLYCAM with GROMACS? It's something I have wanted to try but couldn't see a way to implement the different LJ scaling factors into GROMACS that seem to be required for systems with both carbohydrate and non-carbohydrate molecules.
There are some tricks you can try to get the mixed 1-4 scaling factors
in gromacs. One is to explicitly add the 1-4 interactions as pairs in
the topology and turn off automatic pairs, another is to try a slightly
modified version of the "half epsilon, double pairlist"-method:
I've tried it together with SLipids, and it works fine.
If you're not interested in the rotameric states of omega in your
carbohydrates, you might as well scale the 1-4 interactions the same as
Amber as stated in the Glycam documentation.
> Adam Hardy
> PhD Student
> School of Engineering and Physical Sciences
> Heriot-Watt University
> Edinburgh EH14 4AS, UK
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Jon Kapla [jon.kapla at mmk.su.se]
> Sent: 12 May 2014 12:45
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gen-pairs, nrexcl and [ pairs ] in itp files
> There have been some efforts of trying to implement the 56Acarbo before,
> and there are some files that you might want to take a look at in the
> user contributions section on the Gromacs website. I think the files
> there only delas with 1-4 glycosidic linkages, but I guess it should be
> straightforward to extend it to other connections using the dihedral
> types from the 56Acarbo paper. Anyway the files might come in handy for
> you if you haven't dicovered them yet. I can't say anything about the
> quality of the conversion though, since I haven't used those parameters
> myself, but it seems they use the same approach as you do (and as I did
> a couple of years ago trying to accomplish the same thing, but I swiched
> to Glycam parameters before I finished the project). I guess the best
> thing would be to try to get hold of single point energies from gromos
> and compare them with your conversion.
> Jon Kapla
> On 2014-05-12 12:49, Hardy, Adam wrote:
>> Dear All,
>> I am attempting to make modifications to the Gromos 53A6 forcefield in order to implement the Gromos 56Acarbo forcefield in GROMACS. Most of the modifications are straightforward except for some of the LJ parameters. As well as simple adjustments to most of the 1-4 interaction parameters there is a requirement to implement a) some 1-4 interaction parameters when the 2 and 3 atoms are specific combinations and b) some 1-5 special parameters.
>> As I'm fairly new to GROMACS I was hoping someone could verify my method and clarify one or two things.
>> I would need to set nrexcl to 4 in order to stop the special 1-5 parameters being calculated twice (once "normal" LJ, one "special").
>> In the itp file I would then need to explicitly provide all the special 1-4 and all the 1-5 LJ parameters (in addition to listing the normal 1-4 interaction pairs) as GROMACS cannot look these up in the forcefield files.
>> If gen-pairs is set to yes, does it overwrite parameters given in the itp file? This way I would not have to go through and explicitly list the "normal" 1-4 interaction parameters in the itp file.
>> I hope that is clear.
>> Many thanks in advance,
>> Adam Hardy
>> PhD Student
>> School of Engineering and Physical Sciences
>> Heriot-Watt University
>> Edinburgh EH14 4AS, UK
>> Sunday Times Scottish University of the Year 2011-2013
>> Top in the UK for student experience
>> Fourth university in the UK and top in Scotland (National Student Survey 2012)
>> We invite research leaders and ambitious early career researchers to
>> join us in leading and driving research in key inter-disciplinary themes.
>> Please see www.hw.ac.uk/researchleaders for further information and how
>> to apply.
>> Heriot-Watt University is a Scottish charity
>> registered under charity number SC000278.
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> Top in the UK for student experience
> Fourth university in the UK and top in Scotland (National Student Survey 2012)
> We invite research leaders and ambitious early career researchers to
> join us in leading and driving research in key inter-disciplinary themes.
> Please see www.hw.ac.uk/researchleaders for further information and how
> to apply.
> Heriot-Watt University is a Scottish charity
> registered under charity number SC000278.
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