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

[Justin Lemkul]

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
>>>>>
>>>>> ========================================
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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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-- 
========================================

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

========================================