From: Kevin Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Mon Nov 16 2015 - 10:41:21 CST
Thank you so much for the reply.
In fact, I did regular simulations of a smaller membrane. Currently, the rectangular membrane, that I mentioned in the question, is made from two square equilibrated membrane replicating along the x-axis. But still, after replication, I think the rectangular one should also go through some equilibration runs and that is when I found the annoying problem.
Interestingly, simulation of the smaller square membrane with same parameters did not generate the "bubble".
> On 16 Nov 2015, at 23:48, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
> Hello Kevin, if you replicated a model membrane once in either the x or y direction along its periodicity vector, it should be fine. That, or you can supply specific x and y dimensions to C-GUI.
> There isn't much information about the source of error, but a general recommendation for membrane models is to generate tiny ones, equilibrate them, and then replicate them as needed. This would save both CPU hours (small membranes can be simulated very cheaply)
> and simulation time (oscillations of small membranes have fast time scales, and will equilibrate sooner).
>> On Mon, Nov 16, 2015 at 3:12 AM, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk> wrote:
>> Dear Users,
>> I am doing membrane simulations and I created bilayers from CHARMMGUI. While I do some regular equilibrium protocols on simple membrane in water simulations, I would find my water boxes shrink unusually much towards the z-axis especially after graduate heating up (NVT) and did not recover even after nanoseconds of some more NPT runs.
>> I understand that in sense of PBC, although it looks like my water box was truncated at the eight corners, it actually represents a bubble inside water. I have searched the list and Axel once mentioned this as "safety bubble". Is it normal during the equilibrium of membrane-water simulations? As I do have few cases that the water finally recover like nothing has happened. So I just have to do more NPT runs until it looks normal?
>> One more thing, the situation happened when I simulated a rectangular membrane composed by two square membranes generated from CHARMMGUI (simply as CHARMMGUI does not provide rectangular shapes). Is it due to "badly" piecing membranes together?
>> Thanks in advance.
>> PhD Candidate
>> Department of Physics and Material Science
>> City University of Hong Kong
> Giacomo Fiorin
> Assistant Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213
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