TIP3P is a rigid water model - that bond is supposed to be there. When
I want to get around this I just create separate representations for
O-H1 and O-H2.
-Dan
On Thu, Mar 30, 2017 at 7:04 AM, 吴萌 <wumeng.shanghaitech.edu.cn> wrote:
> Dear All,
>
> I am running a membrane protein MD simulation with Amber14. When load my trajectory in VMD(version 1.9.3), I found the display of water molecules is adnormal: there shown the third bonds between the two hydrogen atoms. I have tried diffrernt drawing method, but the problem is still there. Could it be my water model(tip3p I used) problem or the parameters? If so, how can I fix it.
>
> Any suggestions would be greatly appreciated.Thank you in advance!
>
> Sincerely,
> Wu Meng
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 30 2017 - 05:30:06 PDT
