I would think that too. However, that is not what happens. If you freeze a group it gets scaled according to the box vectors during a npt simulation.
Hence in order to keep the group (in my case a carbon nano tube) of fixed diameter i use position restraints. This protocol works fine with with npt simulations. Now, i wanted to check if i include the bonded interactions in my topology and constrain all the bonds things should not matter at all, since the bonded interactions are redundant in this case. However, that is not the case and the system crashes. If however the bonds are not constrained, things work fine. I know this is a very round about way of getting things done, still i am curious. On Sep 10, 2013 4:12 PM, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 9/10/13 2:59 PM, HANNIBAL LECTER wrote: > >> Hi, >> >> Sorry to bother you again regarding this. But I am not sure, as to why >> freeze + constraints should not work during a NPT simulation? >> >> The update algorithm as shown in the manual does not say anything that >> would fundamentally prevent this. In fact, one can use freezegroups + >> constraints in NVT. What prevents it from running in NPT? >> >> > The use of a barostat requires that the positions of the atoms can be > scaled according to the pressure. Freezing atoms, by definition, makes > them immobile and thus they cannot be scaled. Thus, the two algorithms are > fundamentally incompatible. > > -Justin > > I get the foll. error. >> >> step 0 >> Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 >> -2.7758e+23 >> -2.7758e+23 >> >> Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 >> -2.7758e+23 >> -2.7758e+23 >> >> Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 >> -2.7758e+23 >> -2.7758e+23 >> >> Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 >> -2.7758e+23 >> -2.7758e+23 >> >> Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 >> -2.7758e+23 >> -2.7758e+23 >> >> Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 >> -2.7758e+23 >> -2.7758e+23 >> >> Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 >> -2.7758e+23 >> -2.7758e+23 >> >> Step 1 Warning: pressure scaling more than 1%, mu: -2.7758e+23 >> -2.7758e+23 >> -2.7758e+23 >> Warning: Triclinic box is too skewed. >> Warning: Triclinic box is too skewed. >> Warning: Triclinic box is too skewed. >> ... >> ... >> ... >> Segmentation fault >> >> > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
