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

Jianguo Li ljggmx at yahoo.com.sg
Sun Aug 21 08:29:37 CEST 2011

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, 3882–3893.

best regards,

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 

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, 
Tsinghua, Beijing, China

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