When I've encountered the issue with the ***, i've only usually noticed it
in my restart files and the problem has been solved by turning iwrap on.
Are you writing netcdf trajectories (ioutfm & ntxo)? I understand the
greater level of precision eliminates the typical error associated with
****'s in the restart file.
br,
g
On 12 June 2013 22:07, Benjamin Grant <bdgrant15.gmail.com> wrote:
> Hello,
>
> I’m modeling a carboxylic acid (palmitoleic and linoleic acids) and having
> issues with my MD simulations. I used the RESP methodology along with
> antechamber to get the necessary .prep and .frcmod files. I was able to
> successfully create a box (~25,000 atoms) for each carboxylic acid using
> packmol and tleap. I was also able successfully minimize the structure
> prior to starting my NPT simulations. The simulations seem to start out
> fine but they crash with the energy, temperature and the VDW contributions
> to the energy increasing. I also noticed that when “wrapping first mol”
> appears for the first time in the md.out file, then my mdcrd and rst-crd
> file turn to ‘****’. I have tried turning iwrap off and the problem still
> occurs. Also I’m unable to use VMD to see what is happening since the mdcrd
> file is filled with ‘******’. I have attached my input and output files.
>
> I’m using Amber 12 with all of the bug fixes.
>
> Thanks,
>
> Ben
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 12 2013 - 20:30:03 PDT
