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 list gmx-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 >
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