[gmx-users] Is Gromos43a2X problem?

[Erik Lindahl]

On Tuesday, Mar 11, 2003, at 00:54 US/Pacific, nanyu101 wrote:

> Dear Dr.Erik Lindahl,
>   Sorry to write to you so many letters.
>   I have used your Gromos43a2X force field to simulate the DPPC 
> bilayer for my polyester ion channel.But I have always met some 
> problem in NVT and NPT running.I suppose my minimization is very 
> fine.The minimization information was listed as follows:

[snip]

>
> But when I use minimized structure to run NVT,there are always some 
> problem happened. I think there are some big forces in my lipid 
> bilayer, but how can they exist? Would you like to give me some 
> suggestion? The more detailed log file is in my attachment.
>
This is not a force field problem as far as I can tell.

With LINCS warnings I would suspect you have waters entering your 
membrane between the lipids and the ion channel. Again, look at it and 
see where this molecule is and what is happening to it.

Gromos43a2x is definitely not "my" forcefield btw, it is just a version 
of Gromos with two extra atomtypes suitable for lipid chains. Unless 
you explicitly edited your topology to use these new atom types you are 
using the standard Gromos forcefield.

Cheers,

Erik