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

[James Starlight]

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.

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.


James

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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