[gmx-users] Decreasing of the box size during membrane protein simulation

[Szilárd Páll]

Great discussion!

While (seemingly) small changes in cut-off can give considerable
performance improvements and therefore it is worth considering such tweaks
in simulation settings, these finding highlight the importance of not
changing settings blindly.

Cheers,

--
Szilárd


On Wed, Jan 30, 2013 at 2:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/29/13 11:57 PM, James Starlight wrote:
>
>> Justin,
>>
>>
>> with cut-offs=1.2 both in cpu+gpu or with cpu only I've obtained only
>> small decrease along the Z-dim ( from 10 to 9 nm). With cut-offs 1.0
>> I've obtained decreae from 10 to 8.5. So it might be concluded that
>> the observable is cut-off sensetive.
>>
>>
> Good to know.  Most "normal" systems of proteins in water will probably be
> insensitive to most changes with the new cutoff scheme, but I was
> suspicious about membranes.  I'll have to do some of my own testing, as
> well.
>
>
>  By the way during simulation of such system in gromos-54a7 united atom
>> ( the same number of lipids and water)  ff with 1.2 cut-offs I didnt
>> observed any decrease of the cutoffs.
>>
>>
> Different force fields behave differently.  I wouldn't expect to
> necessarily be able to draw a parallel between different parameter sets
> that inherently use different run parameters, but this is also good to know.
>
> -Justin
>
>
>  2013/1/29 Justin Lemkul <jalemkul at vt.edu>:
>>
>>>
>>>
>>> On 1/29/13 2:19 AM, James Starlight wrote:
>>>
>>>>
>>>> One important point:
>>>>
>>>> in that simulations I've used decreased cut-offs with charmm36 ff
>>>> because that systems have been modelled with CPU+GPU so I had some
>>>> imbalance in cpu\gpu loadings with common (1.2) cutoffs.
>>>>
>>>> rlist           = 0.8           ; Cut-off for making neighbor list
>>>> (short
>>>> range forces)
>>>> rlistlong       = 1.4
>>>> rcoulomb        = 0.8           ; long range electrostatic cut-off
>>>> rvdw            = 0.8
>>>>
>>>>
>>>> Might that affect on the compresbility of my system? Might  I prevent
>>>> such compression by means of changing ref_p or compressibility on the
>>>> Z using  emiisotropic pcoupltype?
>>>>
>>>>
>>> Membranes are very sensitive to cutoff settings.  Can you test by
>>> running on
>>> CPU only with the normal CHARMM cutoff settings?  I would be curious to
>>> see
>>> if the shortened cutoffs produce bad results.
>>>
>>> You should not have to make any special changes to the compressibility or
>>> pressure along Z in order for the simulation to be stable.  What's
>>> happening
>>> to the x and y box vectors?  Is the membrane becoming distorted or
>>> compressed?  Or is it expanding laterally?
>>>
>>>
>>>
>>>  2013/1/29 James Starlight <jmsstarlight at gmail.com>:
>>>>
>>>>>
>>>>> Its intresting that on the same system which was equilibrated longer
>>>>> the decrease on the Z dim was smaller (from 10 to 9nm). By the way
>>>>> does it possible to simulate membrane proteins (with explicit
>>>>> membrane) in the nvt enssemble without explicit barostat ? What
>>>>> options in the mdp should be added for such simulation ?
>>>>>
>>>>>
>>> Certainly you can run in an NVT ensemble if the force field will produce
>>> good results.  Normally NPT or NPAT ensembles are most appropriate for
>>> membranes, depending on the parameterization of the lipids.  Running in
>>> NVT
>>> is as simple as setting "pcoupl = no" while leaving other
>>> thermostat-related
>>> items the same.
>>>
>>> -Justin
>>>
>>>
>>>
>>>>> James
>>>>>
>>>>> 2013/1/28 Justin Lemkul <jalemkul at vt.edu>:
>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 1/28/13 8:45 AM, James Starlight wrote:
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Justin,
>>>>>>>
>>>>>>> yes, 2 A for C atoms.
>>>>>>>
>>>>>>> The dims are 8.68740   8.41864  10.00000
>>>>>>>
>>>>>>>
>>>>>> Well, with such a dramatic change, it should be fairly easy to simply
>>>>>> watch
>>>>>> the trajectory and see what went wrong.
>>>>>>
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>> --
>>>>>> ==============================**==========
>>>>>>
>>>>>> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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