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

[Jianguo Li]

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,
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



__________ Information from ESET NOD32 Antivirus, version of virus signature 
database 6393 (20110819) __________

The message was checked by ESET NOD32 Antivirus.

http://www.eset.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110821/e05d87a1/attachment.html>