From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Jun 13 2011 - 07:50:42 CDT
I would solve this by doing separate runs. You can
access environment variables in TCL using $env(NAME_OF_VARIABLE). So you can
have one conf file and a separate bash scripts that sets
the appropriate environment variables and then runs NAMD.
Also, is the force field precise enough that such small changes in the
dielectric constant are even relevant?
Best regards,
Ajasja
On Mon, Jun 13, 2011 at 14:36, Andres Colubri <andres.colubri_at_gmail.com>wrote:
> Hello,
>
> I'm simulating a heating cycle using the new GBIS model in NAMD, starting
> at T=275 K and ending at T=300K, with increments of 5 degrees.
>
> Since the dielectric of water goes from 88 at 0C to 78 at 28C, the
> simulation script should update the solventDielectric parameter accordingly
> at each temperature step. So I have the following in my config file :
>
> # Heating
> for {set i $temperature0} {$i <= $temperature1} {incr i 5} {
> set temperaturei $i
> langevinTemp $temperaturei
> langevinPistonTemp $temperaturei
> solventDielectric $dielectric($temperaturei)
> }
>
> with:
>
> set temperature0 275
> set temperature1 300
>
> and
>
> set dielectric(275) 87.31
> set dielectric(280) 85.46
> set dielectric(285) 83.61
> set dielectric(290) 81.76
> set dielectric(295) 79.91
> set dielectric(300) 78.06
>
> However, I get this error in the first iteration of the loop:
>
> TCL: Setting parameter solventDielectric to 87.31
> FATAL ERROR: Setting parameter solventDielectric from script failed!
>
> Any help with this will be greatly appreciated.
> Thanks!
>
>
>
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