Re: [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure
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 xiansh...@gmail.com To: gmx-users@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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure
On Fri, Aug 19, 2011 at 8:50 AM, KONG Xian xiansh...@gmail.com wrote: 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? Yes, you have to switch to cutoff for coulomb interaction. I have seen in other publications that they use a regular coulomb with cutoff as large as 2 nm. I am not sure whether there is any advantage in using Reaction field. **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? I have had no problems in using LINCS during local pressure calculation. ** ** 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure
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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
