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

[Justin Lemkul]

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

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