Re: [gmx-users] How to set up constraint distcance pulling
On 6/7/12 9:14 AM, xiaowu759 wrote: Date: Thu, 07 Jun 2012 07:59:27 -0400 From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> Subject: Re: [gmx-users] How to set up constraint distcance pulling To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>> Message-ID: <4fd0979f.4020...@vt.edu <mailto:4fd0979f.4020...@vt.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Thank you very much! On 6/7/12 7:38 AM, xiaowu759 wrote: >> Dear gmxers, >> I am performing COM pulling using GMX4.0.7, to obtain the PMF as a function of >> distance between the COMs of two molecules. However, quite strange resuluts are >> generated, i.e., the distance can not be fixed at the value defined by >>pull_init1. The pull opinions are given below. Could you please tell me how to >> deal with this? Thanks a lot for any reply. >How far away from the target value are the results in terms of COM distance? A: very far, several hundreds vs. 0.8 nm A distance of several hundred nm would indicate to me that the system blew up. >> Chaofu Wu >> ;Pull opinions >> pull = constraint >> pull_geometry = distance >> ;pull_dim = Y Y Y >The comment here has no effect; pull_dim defaults to "Y Y Y." A: Yes >> pull_group0 = r1 > >pull_group1 = r2 > >pull_nstxout = 0 > >pull_nstfout = 5 >> pull_init1 = 0.80 >How does this pull_init1 value compare to the COM separation in the coordinate >file? If the distance is not very close, the constraint algorithm may fail. A: The COM separation in the coordinate file is 0.567 nm, which should be not too larger than 0.80 defined by pull_init1. That's a 29% difference, which is quite large. If constraints are not easily satisfied, the simulation can blow up. Your statement above makes that seem very likely. Your restraint distance should match the actual coordinates very closely, otherwise you will likely need to equilibrate better under e.g. an umbrella potential and relatively weak force constant to obtain better starting structures if you're intent on using a rigid constraint for the PMF calculation. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] How to set up constraint distcance pulling
Date: Thu, 07 Jun 2012 07:59:27 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] How to set up constraint distcance pulling To: Discussion list for GROMACS users Message-ID: <4fd0979f.4020...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Thank you very much! On 6/7/12 7:38 AM, xiaowu759 wrote: >> Dear gmxers, >> I am performing COM pulling using GMX4.0.7, to obtain the PMF as a function >> of >> distance between the COMs of two molecules. However, quite strange resuluts >> are >> generated, i.e., the distance can not be fixed at the value defined by >>pull_init1. The pull opinions are given below. Could you please tell me how to >> deal with this? Thanks a lot for any reply. >How far away from the target value are the results in terms of COM distance? A: very far, several hundreds vs. 0.8 nm >> Chaofu Wu >> ;Pull opinions >> pull = constraint >> pull_geometry = distance >> ;pull_dim = Y Y Y >The comment here has no effect; pull_dim defaults to "Y Y Y." A: Yes >> pull_group0 = r1 > >pull_group1 = r2 > >pull_nstxout = 0 > >pull_nstfout = 5 >> pull_init1 = 0.80 >How does this pull_init1 value compare to the COM separation in the coordinate >file? If the distance is not very close, the constraint algorithm may fail. A: The COM separation in the coordinate file is 0.567 nm, which should be not too larger than 0.80 defined by pull_init1. >-Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Department of Chemistry and Materials Science Hunan University of Humanities, Science and Technology, Loudi 417000, the People's Republic of China (P.R. 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] How to set up constraint distcance pulling
On 6/7/12 7:38 AM, xiaowu759 wrote: Dear gmxers, I am performing COM pulling using GMX4.0.7, to obtain the PMF as a function of distance between the COMs of two molecules. However, quite strange resuluts are generated, i.e., the distance can not be fixed at the value defined by pull_init1. The pull opinions are given below. Could you please tell me how to deal with this? Thanks a lot for any reply. How far away from the target value are the results in terms of COM distance? Chaofu Wu ;Pull opinions pull = constraint pull_geometry = distance ;pull_dim = Y Y Y The comment here has no effect; pull_dim defaults to "Y Y Y." pull_group0 = r1 pull_group1 = r2 pull_nstxout = 0 pull_nstfout = 5 pull_init1 = 0.80 How does this pull_init1 value compare to the COM separation in the coordinate file? If the distance is not very close, the constraint algorithm may fail. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] How to set up constraint distcance pulling
Dear gmxers, I am performing COM pulling using GMX4.0.7, to obtain the PMF as a function of distance between the COMs of two molecules. However, quite strange resuluts are generated, i.e., the distance can not be fixed at the value defined by pull_init1. The pull opinions are given below. Could you please tell me how to deal with this? Thanks a lot for any reply. Chaofu Wu ;Pull opinions pull = constraint pull_geometry = distance ;pull_dim = Y Y Y pull_group0 = r1 pull_group1 = r2 pull_nstxout = 0 pull_nstfout = 5 pull_init1 = 0.80 -- Department of Chemistry and Materials Science Hunan University of Humanities, Science and Technology, Loudi 417000, the People's Republic of China (P.R. 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
