[gmx-users] problem of GLUP

Albert mailmd2011 at gmail.com
Tue Jan 21 16:36:27 CET 2014

Hi Justin:

thanks a lot for the comments.

This residue is a standard Glu, it is protonated which need to change 
the name into GLUP so that gromacs can process it as -COOH instead of 
-COO-. In principle, it should be included in the "protein" group, but 
it seems that it doesn't according to the errors from grompp.

I checked the cpu nodes in my cluster, and I don't find anything wrong. 
I also submit another system into MD simulations, and the efficiency 
looks good. The NVT step for other system can obtain 40ns/day, but this 
only get 2ns/day for this one.... I don't know what's happening

thanks a lot


On 01/21/2014 03:59 PM, Justin Lemkul wrote:
> Consider step #5:
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field 

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