[gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure
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.
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.
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.
Tsinghua, Beijing, China
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