On 5/04/2011 3:57 PM, ahmet yıldırım wrote:
Dear Tsjerk,Hi Ahmet, As suggested, it's better to break up your molecule into smaller charge groups. Note that charge groups don't need to have zero charge, nor integer charge. In your case, I'd suggest two COH groups for EDO, which will have zero net charge each, and for TRS I'd take the COH groups as separate charge groups. I also note that the COH groups, although chemically identical - H3NC(COH)3, right?-, have different charges. That doesn't seem proper. Hope it helps, Tsjerk nonrevised .itp file: EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 1 0.031 1.0080 3 CH2 1 EDO CAA 1 0.080 14.0270 4 CH2 1 EDO CAC 1 0.080 14.0270 5 OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 1 0.031 1.0080 nonrevised .itp file: EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 1 0.031 1.0080 3 CH2 1 EDO CAA 1 *0.000* 14.0270 4 CH2 1 EDO CAC 1 *0.000* 14.0270 5 OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 1 0.031 1.0080can you show me on the itp file? how do I seperate two COH groups? Please help me
We didn't say to use zero *charges*. We said you need small charge groups. Since EDO is neutral, then by symmetry each half must also be neutral.
Have a look at the way charge groups are used in the .rtp file for your forcefield. You need to do similar things. If you don't understand the file formats yet, you need to read up on chapter 5 of the manual.
Mark
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