> I have tried ntt=1.
> But it shows an error
> ntt must be 3 or 4 if gamma_ln > 0
>
> *** input error(s)
Just remove gamma_ln from the input file as well.
> Keep DNA fixed with weak
> restraints
> 10.0
> RES 1
> 20
> END
This looks reasonable. You could try reduce the restraint weight to 2.0 or
so but I doubt that is the issue here. What are you using as the reference
structure? (-ref on the command line). Try pointing it to the minimized
structure rather than the original inpcrd structure.
Also set ntpr =1 and ntwx =1 and nstlim = 1000 and run it and then visualize
the output and see if you can see what might be going wrong early on. Also
take a look at the energies from the first few steps of MD and also from the
end of the minimization. The end of the minimization will give you an idea
of which atom has the highest force on it so you know where to look when
visualizing the output.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Mon Sep 12 2011 - 23:00:06 PDT
