[gmx-users] Re: Water molecules cannot be settled: V-rescale is the cause

Mark Abraham Mark.Abraham at anu.edu.au
Thu Sep 20 09:09:55 CEST 2012

On 20/09/2012 4:34 PM, Ladasky wrote:
> Justin Lemkul wrote
>> So the initial equilibration was NPT?
> Yes.
> Justin Lemkul wrote
>> Did you ever try simply running NVT with
>> either Berendsen or V-rescale before applying any type of pressure
>> coupling?
> No, I haven't, and I don't remember seeing that described in any work flow.

Point 8 of 
mentions it.

> Justin Lemkul wrote
>> Immediate application of NPT is often unstable for a variety of reasons,
>> not
>> necessarily the temperature coupling algorithm.
> All right, that's useful information.  But what I am doing here is ripped
> from a tutorial file, and modified as little as possible.  I try not to
> change things that I do not yet understand.  My source for the MDP files was
> the lysozyme tutorial shell script that accompanied GROMACS 3.3.  If there
> are procedures in that tutorial that are obsolete, I guess I'm finding that
> out the hard way.

Using any single source can lead to problems. Sometimes tutorials are 
deliberately stripped down to produce a numerical result in quick time, 
but not via a method that is useful for a real problem. Material gets 
dated and busy authors don't get paid for keeping them up to date, 
unfortunately. Doing all the tutorial material you can find, even if you 
think the topic irrelevant, will add do the general knowledge you need. 
Further clues can be found in methods reported in published work, 
particularly relevant if on systems similar to yours, or by people you 
can see are highly experienced with GROMACS because they've published 
results from using it for a while.


> Justin Lemkul wrote
>> Anyone is welcome to contribute to the wiki; it is a community project,
>> after
>> all.  I would also be interested to see if it can be demonstrated that NPT
>> with
>> V-rescale + Berendsen is unstable after an independent NVT simulation with
>> either method.
> I may take the time to try that experiment later.  I'll report back with any
> findings.
> Thanks for your help!
> --
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