[gmx-users] 答复: Re：the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure

[KONG Xian]

Thanks for your important advice, I am extending my simulation to 60ns, if it is still not long enough, I’ll extend another time. Thank you.

 

 

发件人: Jianguo Li [mailto:ljggmx at yahoo.com.sg] 
发送时间: 2011年8月22日 9:52
收件人: KONG Xian
主题: Re: Re：the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure

 

 

Thanks for your kindly reply. 

I used the LINCS calculated the pressure field. The distinct between protein and the lipid bilayer is obvious from the pressure field. 

But the lipid bilayer and the water is not very obvious , they seems to be a uniform from the pressure field calculated. As in Ollila’s original paper: 3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes, there is an distinct separation region between membrane and the water.

Maybe the LINCS is the problem.

Another problem is perhaps the localpressure software is for CG model? My model is all-atom model and the simulation time length is not long enough, maybe this is the cause of the results?

>From my limited experience, the local pressure calculation converges very poorly. It takes more than 50 ns of production run in my case to get a converged profile. You can divide the production run into several sub-trajectories to judge the convergence.



KONG Xian

2011/8/21

 

Hi, Kong Xian,

 

It is better to use SHAKE instead of LINCS since LINCS does not directly yield pairwise forces, as shown in the paper: Erik Lindahl and Olle Edholm. Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. JOURNAL OF CHEMICAL PHYSICS, VOLUME 113, NUMBER 9, 3882b3893.

 

best regards,

Jianguo 

 

 

 

 

________________________________

From: KONG Xian <xianshine at gmail.com>

To: gmx-users at gromacs.org

Sent: Friday, 19 August 2011 23:50:01

Subject: [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure

 

I have sent this email days ago, but I got no answer.

Hope someone would saw it this time. 

Sorry for disturbing.

Dear all:

         I am using gromacs-4.0.2_localpressure to calculate the local pressure of my system.

         I have a question.

         When rerun the mdrun from gromacs-4.0.2_localpressure I used a new .mdp file. There are some changes of the new .mdp file according the original one. I have 2 questions:

1.      I changed the The coulomb interaction type from PME to reaction field 

with epsilon_r=1 epsilon_rf=78;  Is this change feasible?

2.      I used LINCS for all bonds in the simulation, and I still use the LINCS 

for all bonds when calculate the local pressure. Is this way right? 

 

Thanks for any reply.

Best wishes,

KONG Xian

Tsinghua, Beijing, China

 

 



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