[gmx-users] Decreasing of the box size during membrane protein simulation
jmsstarlight at gmail.com
Tue Jan 29 08:19:46 CET 2013
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?
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 ?
> 2013/1/28 Justin Lemkul <jalemkul at vt.edu>:
>> On 1/28/13 8:45 AM, James Starlight wrote:
>>> 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 A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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