[gmx-users] How to add two different "defaults" parameters in topology file

[Justin Lemkul]

On 2/5/20 12:54 PM, mbhendle wrote:
> Hello all,
>
> I am trying to simulate polymers in tip4p-ice and for that I need to set
> two different "defaults" parameters for polymer chain and TIP4P-ICE in
> topology file. The "moleculetype" for Polymer chain and water is also
> different:
>
> [ defaults]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ    (for polymer)
> 1                  3             yes        0.5         0.5
>
> [ defaults]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ    (for TIP4P-ICE)
> 1                  2             no          1             1
>
> [moleculetype]
>
> ;Name     nrexcl
>
> Other       3  ;(Polymer)
>
> SOL          1  ;(TIP4P-ICE)
>
> For this purpose, I have created two different ".itp" files for polymer
> chain and TIP4P-ICE. But while running "gmx grompp" gromacs is showing
> "Invalid order for directive moleculetype". I also tried putting two
> defaults parameters into ".top" file itself. But it also showed error.
>
> Please suggest how to do it.

You can't have two [defaults] directives. The gen-pairs, fudgeLJ, and 
fudgeQQ values only affect 1-4 interactions, which are not applicable to 
water, so I don't understand why they're relevant. You certainly can't 
mix different combination rules in a system, but you could specify 
different nonbonded parameters via [nonbond_params] rather than trying 
to specify different combination rules.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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