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 <[email protected]> To: [email protected] 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
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