so to clarify, try with ioutfm=1 and ntxo=2, iwrap=0
On 13 June 2013 04:11, ET <sketchfoot.gmail.com> wrote:
> 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
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
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Received on Wed Jun 12 2013 - 20:30:03 PDT
