Re: mail reg constraint force

From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri Jun 22 2018 - 08:14:08 CDT

The answer depends entirely on your system. What is your atom selection
within the protein and what are their bfactors (or whatever value you are
using)? Note that the applied force constant is constraintScaling*bfactor.
For early stage equilibration it would not be unreasonable to apply
restraints to all heavy atoms.

HTH,
BKR

On Fri, Jun 22, 2018 at 8:04 AM, Vidhya Sankar <
vidhyasankar7928_at_remove_yahoo.com> wrote:

> Dear namd user
> i would like to constraint protein atoms above
> lipid leaflets but when i run equilibration, the protein molecules buried
> inside lipid leaflets.. Which parameters should i increase to keep
> my protein molecules fixed above lipid leafletes throughout equilibration
> in namd configuration file
>
> The deault value i am using in configuration file
>
> consexp 2
>
> constraintScaling 1.0
> with regards
> S.Vidhyasankar
>

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