Re: Running AMBER FF with NAMD 2.8-CUDA

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Oct 19 2011 - 09:23:32 CDT

On Wed, Oct 19, 2011 at 3:37 PM, Nicholas M Glykos <glykos_at_mbg.duth.gr> wrote:
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>> Info: MASS DENSITY = 10.7355 g/cm^3
>> Info: ATOM DENSITY = 1.05952 atoms/A^3
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> That doesn't look good ...

True. That confirms my suspicion: should leap be run with special
flags (for example for TIP3 water)? I just took the .prmtop/.inpcrd
files mfrom the tutorial, and they surely work with AMBER.

fp
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> --
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>          Dr Nicholas M. Glykos, Department of Molecular Biology
>     and Genetics, Democritus University of Thrace, University Campus,
>  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
>    Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
>
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