Re: membrane simulation ERROR rattle algorithm

From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Jul 06 2011 - 10:06:03 CDT

Try to increase temp slowly or first heat the membrane up to desired
temperature. Then follow small minimization and equilibrated the whole
system.

ps: Check the rattle atom position. if it is part of membrane then you have
to minimize for lone and slowly increase the temperature. In most of the
membrane simulation use timestep of 1fs/step Otherwise before minimization
fix the protein and heat the mebrane so that it will wrap around the
protein.

On Wed, Jul 6, 2011 at 6:37 AM, Ajasja Ljubetič
<ajasja.ljubetic_at_gmail.com>wrote:

> Hi,
>
> Thanks - so the atoms do not look strange - nor on top of each other.
>>
>
> Are they near the periodic boundary?
>
>
>
>> If I run the whole system without any constraints on headgroups,
>> water, or protein it is not a problem and I can run with 2 fs - I find
>> this a little bit strange
>>
>> Hmm, did you check the positions of the head groups in the file you are
> using for the constraints?
>
>
>> Should I run longer(more minimization?) or should other things be test
>> before this?
>>
>>
> Well, I'd just equlibrate for a ns or so with the on fs step (while
> gradually releasing the constraints with *constraintScaling*). After
> equilibration you can switch to a 2 fs step.
>
> Regards,
> Ajasja
>

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