[gmx-users] About Umbrella sampling

[Justin A. Lemkul]

On 6/7/12 12:26 PM, vidhya sankar wrote:
> Dear justin Thank you for your previous Valuable reply.
> To do umbrella sampling should i run more number of steps than i run in Umbrella
> pulling ?

That depends on how many steps were used for the pulling.  Also note that the 
pulling step represents just one possible way to generate initial configurations 
and is not necessarily even required, so you shouldn't necessarily base a whole 
lot on this process.

> otherwise if i use lesser number of steps in Umbrella sampling than pulling will
> it affect result

You shouldn't try to connect the two.

> Is there is any rule between number of steps and dt in umbrella pulling and
> umbrella sampling?
>

The same rules as any simulation apply.  Parameters like dt are chosen based on 
what gives a stable result.  The length of the simulation depends on your 
convergence criteria.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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