[gmx-users] Re: WARNING concerning lipid.itp

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Feb 5 22:13:50 CET 2008

> And again I will support myself   :-)

If you want to get more replies, you should include some more detailed  
information and also search the archives first (e.g. you might have  
found this:  
http://www.gromacs.org/pipermail/gmx-users/2002-July/001986.html by  
searching Overriding LJ-14 parameters)

> So, as I learnt so far, for this effect the topology
> file is responsible.
> In the included force fields the described LJ 1-4
> parameters does not correspond to the LJ
> parameters of the OW OW interaction of the
> lipid.itp which gets included after these force
> fields, I guess... and thus it gets exchanged after
> all....

Download the new lipid.itp. I don't find OW OW pairtypes specified in  
my version of lipid.itp at all.

I find line 703 to be the following:
    OW   LNL     1 3.72700e-04  4.07400e-07

As for the information that you should be providing... put yourself in  
our shoes. We have no idea what the .top looks like so how can we give  
you some tips about parameters being overwritten.

> mark
> Wissensbund at gmx.net wrote:
>> Hello.
>> I am a gmx-newcomer and I try to start simulating
>> bilayer membrane systems for which I need to include
>> the lipid.itp of Thieleman into my .top-file.
>> After processing grompp I get one WARNING concerning
>> the lipid.itp...
>> WARNING 1 [file "lipid.itp", line 703]:
>>   Overriding LJ-14 parameters,
>>   old: 0.0026171 7.4158e-07 0 0
>>   new: OW OW 1 3.31400e-04 3.36000e-07
>> Could someone please explain, why this happens?
>> So, LJ is the Lennard-Jones parameter, but why
>> gmx has to change it, and why this is necessary
>> only for line 703 again and again??
>> Thanx for your help in advance.
>> newcomer Mark

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