From: Brian Radak (brian.radak_at_gmail.com)
Date: Sat Jan 25 2020 - 10:00:20 CST
I can't specifically speak to such old versions of NAMD, but a useful AMBER
resource on the matter can be found at
http://ambermd.org/namd/namd_amber.html
The most important differences are the 1-4scaling, cutoff (AMBER defaults
to 8), switching (AMBER uses none), and LJcorrection (AMBER defaults to
on).
AMBER also uses a smaller default SHAKE tolerance and has a different way
of determining Ewald coefficients.
Lastly, the Coulomb coefficient is different between the two codes, but
this may be accounted for in the RTF file I suppose?
HTH,
BKR
On Thu, Jan 23, 2020, 10:01 AM <nikolaev_at_spbau.ru> wrote:
> Dear collegues,
>
> I want to use charmm-formatted amber parameters in NAMD-2.13. I found that
> I need to scale 1-4scaling 0.833333333, add scnb 2.0, if I use the amber
> .parm7 files. I also found that for NAMD.2.7 I would have to modify
> src/common.h file.
>
> Should I modify anything in .conf file, if I use charmm-formatted amber
> parameters in NAMD-2.13?
>
> I use it like this now:
>
> paraTypeCharmm on
> parameters ./par_amber14.inp
> temperature $temperature
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 0.83333333
> cutoff 16.0
> switching on
> switchdist 14
> pairlistdist 17.0
>
> zeromomentum on
> useSettle on
> rigidTolerance 1.0e-8
>
>
>
> Best regards,
> Dmitrii
>
>
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