[gmx-users] problem of GLUP
mailmd2011 at gmail.com
Tue Jan 21 16:36:27 CET 2014
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:
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