Re: [gmx-users] Freeze + NPT + constraints
In reality, what we should do is make it a fatal error, because truly, frozen groups should be used very sparingly and certainly never with NPT. It just doesn't make sense. I understand what you're trying to accomplish, but the underlying theory becomes flawed. Agreed Mark -- 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] Freeze + NPT + constraints
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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Freeze + NPT + constraints
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 listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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
Re: [gmx-users] Freeze + NPT + constraints
On 9/10/13 5:17 PM, HANNIBAL LECTER wrote: 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. Are the positions of the atoms actually changing? If they are, that's a bug. It shouldn't happen, and in previous version of Gromacs, I know it didn't. Can you point to the code that is making this happen? 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. Constraints and barostats both try to modify coordinates. The freezegrps mechanism prevents modifications of coordinates, so what you're trying to satisfy is a barostat that wants to scale coordinates (you say that is accomplished somehow; I would like to see the evidence so the issue can be addressed) and a constraint algorithm that wants to satisfy bond lengths. One of those is bound to fail. I can imagine that if the initial configuration perfectly satisfied the constraints, then maybe the run could proceed (because freezegrps and constraints wouldn't be fighting one another), but I still can't get my head around any way that you could satisfy freezing and a barostat. In reality, what we should do is make it a fatal error, because truly, frozen groups should be used very sparingly and certainly never with NPT. It just doesn't make sense. I understand what you're trying to accomplish, but the underlying theory becomes flawed. -Justin 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 listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
