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

[James Starlight]

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?

James

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 ?
>
>
> 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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