From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Jun 03 2013 - 09:16:05 CDT
Hello James,
1) run for as few steps as you like, using the options "constraints" (aka
position restraints in NAMD lingo).
2) Even under optimal conditions, either the GPUs or the CPUs may be only
partially utilized, because the balance between them is complex, and a
strong limitation is imposed by the motherboard's bus speed. Just look for
the configuration with the lowest time per step.
3) For development of CHARMM-format parameters, the best resource is Alex
MacKerell's webpage.
Giacomo
On Mon, Jun 3, 2013 at 10:08 AM, James Starlight <jmsstarlight_at_gmail.com>wrote:
> Dear NAMD users!
>
>
> Recently I've tried to launch my first simulation on NAMD :) (previously
> I've used Gromacs ).
> My questions:
>
>
> 1) Typical gromacs simulation consist of energy minimization +
> equilibration in NPT ensemble (with position restraints applied on each
> atoms of protein) + production run.
>
> As I understood minimization should explicitly defined in the conf file
>
> # Minimization
> minimize 100
> reinitvels $temperature
>
> run 5000000
>
> but what about equilibration stage ? How I can perform short simulation
> with the applied porses prior to the production run?
>
>
>
> 2) How I can monitor total performance of the GPU utilized in the
> simulation assuming that I use CUDA.
>
> 3) I have parameters ( prm and inp files) for some non-standard residue (
> GFP chromophore). for this protein I'd like to make model (including
> protein covalently bonded to the chromophore and solvent) and perform
> simulation. Could you provide me with the example or short tutorial for
> such task?
>
>
>
> Thanks for help,
>
>
> James
>
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