AMBER Archive (2008)

Subject: Re: AMBER: High force constant for MD ???

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Jul 23 2008 - 06:02:13 CDT

yes that is very high and may cause problems.
maybe it is better to determine why you need such a strong force
constant- why does the sugar have such large desire to become distorted?
it sounds like you have a problem in the parameters, and if it takes
700 kcal/mol force constant to fix it then things are really wrong.
usually the underlying parameters are several kcal, not hundreds.
I think for us to help more we need to know more about your
parameters for the carbohydrate and also what you mean by "valid"
conformation. my concern in reading a paper about such work is that
if you need 700 kcal to fix the part you know is "wrong", then probably
the part you are trying to learn from the simulation is also wrong.
carlos

On Wed, Jul 23, 2008 at 5:49 AM, Waqas Nasir <nasirwaqas1983_at_yahoo.com> wrote:
> Hi,
>
> Hope every thing is working fine at your side.
>
> Well, I am running minimization and MD studies using sander module of amber
> version 8 on protein carbohydrate complex. I have to fix the sugar ring so
> that the conformation remains valid till the end. In minimization, I first
> tried the force constant of 50 K-Cal/Mol-A**2 which didnt work that well and
> the ring was distorted, then I jumped to a higher value of 700 (just to make
> sure that the ring does not move!) which worked out in the end.
>
> Now I am attempting to do the equilibration. Is there any problem if I use
> the same force constant of 700 in equilibration and MD as well (just on the
> sugar ring not on the whole complex). I read in the tutorial that its not
> recommended to use high force constants in MD simulations. Any body with any
> comments or suggestions?
>
> Thanks alot for reading,
> Stay blessed!
>
> Regards,
> Waqas.
>
>
> PS: Thanks Lachele, for your extensive and worthed help!
>
>
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