On 2012-09-06 02:46:21PM +0200, Bogdan Costescu wrote: > On Wed, Sep 5, 2012 at 8:37 PM, Peter C. Lai <p...@uab.edu> wrote: > > Could be a result of not setting x/y compressibility = 0 as the manual > > suggests you should do... > > As one who has also tried to use walls recently, I've also found this > statement in the manual, but no further explanation. Anyone cares to > expand on it ? > > For testing, I've recently performed a run with compressibility=0 for > z and non-zero for x/y (so, exactly opposite to what the manual > suggests :)). The box deformed as expected in x/y and the pressure > seemed to be maintained correctly. Is there some reason for which this > would be a random (i.e. not easily reproducible) result ? Or are there > some less obvious problems with it ?
I am trying to use walls with lipid bilayers. I once also applied a non-zero compressibility to x/y , and my bilayer physically collapsed in less than 1ns, although the simulation appeared to be otherwise nominal. Another thing I noticed was that the value of wall_density is important, since a small leakage past the wall may not be noticeable until you exceed 1-10ns and that will quickly drop volume to 0 and make it look like x/y has collapsed (and cause a system crash due to exceeding pme/dd tolerances). -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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
