[gmx-users] 1-4 interactions in a small molecule are missing

Lee-Ping Wang leeping at stanford.edu
Sat May 23 19:53:30 CEST 2015 

Thanks, Bogdan.  I didn't find that message when I Google-searched my
question.  Now that there are two instances of this question / answer,
future users could find it more easily.  :)

- Lee-Ping

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
Bogdan Costescu
Sent: Saturday, May 23, 2015 10:52 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] 1-4 interactions in a small molecule are missing

Well, a search on this list would have yielded a longish message I wrote,
explaining how this works:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/0
77005.html

(but look also at other messages in that thread) where this is also
expressed:

"It's the user's responsibility to add all needed (1-4 in case of
OPLS-AA) pairs to the [pairs] section; pdb2gmx normally does this, but if
you build the topology through other means then you have to make sure these
pairs are generated."

Cheers,
Bogdan

On Sat, May 23, 2015 at 7:42 PM, Lee-Ping Wang <leeping at stanford.edu> wrote:
> Hi Mark,
>
> Ah, thanks for the explanation.  Everything makes sense now.
>
> I think that the name of "gen-pairs" could be changed to something 
> like "gen-pair-parameters", because "gen-pairs" implies that the 
> actual list of pairs is being generated.
>
> - Lee-Ping
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf 
> Of Mark Abraham
> Sent: Saturday, May 23, 2015 10:40 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] 1-4 interactions in a small molecule are 
> missing
>
> Hi,
>
> I think that is the behaviour, though the wording of manual 5.7.1 
> leaves a lot to be desired... I'd fix it, but I've never played with 
> the feature, nor looked at that code!
>
> Mark
>
> On Sat, May 23, 2015 at 7:34 PM Lee-Ping Wang <leeping at stanford.edu>
wrote:
>
>> Hi Mark,
>>
>> Thanks for the explanation, and I tried your suggestion.  The energy 
>> with setting "nrexcl = 2" is different from "nrexcl = 3", but 
>> changing fudgeLJ and fudgeQQ does not affect the energy in either 
>> case.  There are still no
>> Coulomb-14 and LJ-14 energy terms from g_energy.
>>
>> I think what's happening is that when I set "nrexcl = 2", Gromacs 
>> calculates the full nonbonded interaction between pairs of atoms 
>> separated by 3 bonds, rather than a "1-4 interaction" which is 
>> counted as a different energy term and is scaled by fudgeLJ and fudgeQQ.
>>
>> This leads me to conclude that there are no 1-4 pairs created when 
>> gen_pairs=yes in grompp.  gen_pairs=yes only generates the pair 
>> _parameters_ from the atom types, but not the pairs themselves.  
>> There are only 1-4 pairs when there's a "[ pairs ]" section 
>> explicitly defined in the topology file, which pdb2gmx auto-generates 
>> for proteins for example.  Is this the expected behavior?
>>
>> Thanks,
>>
>> - Lee-Ping
>>
>> -----Original Message-----
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
>> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf 
>> Of Mark Abraham
>> Sent: Saturday, May 23, 2015 9:58 AM
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] 1-4 interactions in a small molecule are 
>> missing
>>
>> Hi,
>>
>> nrexcl = 3 means to exclude non-bonded interactions up to 3 bonds 
>> away, so you're getting the "no 1-4 interactions" behaviour for which 
>> you inadvertently asked. So set it to 2 and see how you go.
>>
>> Mark
>>
>> On Sat, May 23, 2015 at 6:44 PM Lee-Ping Wang <leeping at stanford.edu>
>> wrote:
>>
>> > Hi everyone,
>> >
>> >
>> >
>> > I've been trying to understand an issue I've had with a simple 
>> > molecule in Gromacs (just 20 atoms) where gen_pairs=yes, nrexcl=3 
>> > and all of the atoms carry some charge.  The system is non-periodic 
>> > with no cutoff.  This is a minimal test case derived from a more 
>> > complex system (a lipid bilayer) where I first saw this issue.
>> >
>> >
>> >
>> > My issue is that there is no "Coulomb-14" or "LJ-14" energy term, 
>> > and the potential energy does not depend on my setting of fudgeLJ 
>> > and
>> fudgeQQ.
>> > When
>> > I run gmxdump on my .tpr file, it does not output any LJ14
interactions.
>> > It
>> > does print out the value of fudgeQQ but this value doesn't have an 
>> > effect on the potential energy.
>> >
>> >
>> >
>> > I thought that this molecule should have some 1-4 interactions 
>> > because there are several pairs of atoms that are separated by 
>> > three bonds, and both atoms have nonzero charge and LJ parameters.  
>> > I also wrote a Python script to calculate the Coulomb and LJ energy 
>> > just for this system, and I confirmed that Gromacs was behaving as 
>> > if fudgeLJ and fudgeQQ were both set to zero.
>> > My example calculations are archived and documented here:
>> > https://dl.dropboxusercontent.com/u/5381783/zerotor_excl3.tar.gz
>> >
>> >
>> >
>> > If someone more experienced with Gromacs could look at my files and 
>> > explain how I'm misunderstanding the generation and treatment of 
>> > 1-4 pairs in Gromacs, I would highly appreciate it.
>> >
>> >
>> >
>> > Thanks,
>> >
>> >
>> >
>> > -          Lee-Ping Wang
>> >
>> >
>> >
>> > --
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