From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Jul 16 2015 - 17:18:20 CDT
Indeed there is. Just do
minimize 1000
to minimize fo 1000 steps. Adjust as needed.
Sometimes I find it useful to set a high damping value (high viscosity) for
the langevin thermostat and do cycles of minimization and short runs.
Something similar to the example below.
All the best,
Ajasja
_____________________
langevin on ;# do langevin dynamics
langevinDamping 10 ;# damping coefficient (gamma)
langevinHydrogen yes
langevinTemp 300
#consider also using constraints
constraints on
consref $strucname.pdb
conskfile $strucname-ends.fix
conskcol b; #backbone 1
constraintScaling 10
minimize 160
run 60
minimize 160
run 60
minimize 160
run 60
constraintScaling 1
minimize 160
run 60
minimize 160
run 60
constraintScaling 0
minimize 160
run 100
minimize 160
run 100
minimize 160
run 100
On 16 July 2015 at 22:37, Simon Kit Sang Chu <simoncks1994_at_gmail.com> wrote:
> Hi,
>
> I have been struggling in a unstable system. The VDW and electric
> potential explode right at the beginning. Therefore I want to do the
> minimization without MD. Is there such function in NAMD? Where to specify
> it?
>
> Thanks,
> Simon
>
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