[gmx-users] Is minimization and equilibration needed for umbrella sampling?

Justin Lemkul jalemkul at vt.edu
Wed Jan 15 03:15:23 CET 2020



On 1/13/20 9:22 AM, Qing Lv wrote:
> Thank you, Justin. I start each run by randomly generate velocities at 300K, and each run is quite stable. So, is it appropriate to regard the first 20 ps (this is a QM/MM MD) of each run as the equilibration and just discard this 20 ps in the final wham analysis?

If 20 ps is sufficient equilibration, sure.

-Justin

>
> Best,
> Qing
>
>
>
> At 2020-01-13 21:29:23, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>
>> On 1/10/20 11:02 AM, Qing Lv wrote:
>>> Dear Colleagues,
>>>
>>>
>>> I am doing a QM/MM umbrella sampling to calculate the PMF of an enzymatic reaction. The initial coordinates (with solvents and ions) for each sampling window were extracted from previous trajectories. The reaction coordinate (bond length difference) of each initial frame was closed to the center of the window. So, need I do energy-minimization and equilibration for each window? Since each initial conformation has no bad clashes (actually they can run MD well without minimizations) and is closed to the window center, I cannot understand why minimization and equilibration are still needed (as a lot of references do so).
>> I don't think minimization is essential, but unless you saved the full
>> state (including velocities) for each snapshot, then you need to
>> re-equilibrate. Otherwise you're either starting from T=0 K (gen-vel=no)
>> or a random state that is not necessarily stable (gen-vel=yes).
>>
>> -Justin
>>
>> -- 
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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