Re: [gmx-users] No default Ryckaert-Bell. types
Hi Dan and all guys, Thanks for your answers. I find that the OPLS-AA force field does not contain the dihedral force-field parameters of the Chain_C. Actually, my Chain_C was a hydroxyapatite (HAP, inorganic material) model. I also notice that the bond types of HAP in the ffbonded.itp file are missing. Following are some parameters from my ffbonded.itp file. [ dihedraltypes ] ; ijkl func coefficients C3 CT NT C3 3 1.78866 3.49154 0.53555 -5.81576 0.0 0.0 ; (From wildcard) amine all-atom [ bondtypes ] ; ij func b0 kb OWHW 10.09572 502080.0 ; For TIP4F Water - wlj 1/98 My question is that what are the meanings of the i, j, k, l, func, coefficients, b0, and kb? How to find the values of those of HAP? Just list some [bonds] and [dihedrals] of my Chain_C as follows. [ bonds ] O1 P27 O10 P27 O13 P27 O14 P27 O2 P28 [ dihedrals ] O1P27 O10 O13 O1P27 O10 O14 O1P27 O13 O10 O1P27 O13 O14 O1P27 O14 O13 Thanks for your time and any suggestions. Kind regards, Baolin -- Original -- From: "Dan Gil"; Date: Tue, Aug 14, 2018 04:39 AM To: "gmx-users"; Subject: Re: [gmx-users] No default Ryckaert-Bell. types Hello, This is telling you that the OPLS-AA force field does not have the dihedral force-field parameters for your molecule (topol_Other_chain_C.itp) of the Ryckaert-Bell type. Your exact problem might be: (1) There is something wrong with the molecule topology. (2) OPLS-AA really doesn't have the dihedral force-field parameters, and you need to use another force-field. If your molecule is a simple hydrocarbon, it is unlikely that OPLS-AA has missing parameters. Dan On Sat, Aug 11, 2018 at 10:52 AM, Baolin Huang wrote: > Dear All, > I experienced an error as follows: (I used the OPLS-AA force field) > ERROR 48600 [file topol_Other_chain_C.itp, line 144934]: > No default Ryckaert-Bell. types > > > Anyone can help? > Kind regards, > > > -- > > Dr. Baolin Huang > Lecturer, School of Life Sciences, Guangzhou University > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] 回复:Re: 回复:Re: Mixing rule between organic and inorganic units
Hi all， That is a pure simulation work，no experimental data. The reviewer doubt the Lorentz-Berthelot combination rule for calculating the interaction energy between BMP-2 and HAP. I have to persuade the reviewer that the mixing rule works well in the BMP-2/HAP system. Thanks for your help. Baolin -- 该邮件从移动设备发送 --原始邮件-- 发件人："Justin Lemkul "; 发送时间：2018年8月13日(星期一) 晚上11:31 收件人："gmx-users" ; 主题：Re: [gmx-users] 回复:Re: Mixing rule between organic and inorganic units --- On 8/13/18 11:28 AM, Baolin Huang wrote: > Hi， > I calculated the interaction energy（actually van der Waals part and > electrostatic part），Rg，RMSD，and RMSF. > regards， I wouldn't think any of those are necessarily meaningful (interaction energy almost certainly isn't, and a decomposition between vdW and electrostatics definitely means nothing). Rg might be useful if there is an experimental quantity with which to compare. The broader point is: you have to prove that your physical model reproduces some known quantity before you can start making predictions about others. If there's a known defect in treating energetics (which should be compared with free energies of binding, etc.) then none of the outcomes you generate are reliable. That seems to be your reviewer's problem. -Justin > -- > 该邮件从移动设备发送 > > --原始邮件-- > 发件人："Mark Abraham "; > 发送时间：2018年8月13日(星期一) 晚上11:02 > 收件人："gmx-users" ; > 抄送："gromacs.org_gmx-users "; > 主题：Re: [gmx-users] Mixing rule between organic and inorganic units > --- > Hi, > > What experimental data can you replicate to show the model is valid? > > Mark > > On Mon, Aug 13, 2018, 17:34 Baolin Huang wrote: > >> Dear All, >> I studied the interactions between BMP-2 (protein) and hydroxyapatite >> (HAP, inorganic material) by GROMACS with the OPLS-AA force field. The >> mixing rule was the Lorentz-Berthelot combination. A reviewer commented >> that 'The interaction of organic molecule on inorganic material needs >> careful treatment in classical MD simulation since it is well known that >> the mixing rule does not work well.' >> How to answer this comment? How to validate the mixing rule is suitable >> to calculate the interaction between organic and inorganic units? >> >> >> Best wishes, >> >> -- >> >> Dr. Baolin Huang >> Lecturer, School of Life Sciences, Guangzhou University >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] 回复:Re: Mixing rule between organic and inorganic units
Hi， I calculated the interaction energy（actually van der Waals part and electrostatic part），Rg，RMSD，and RMSF. regards， -- 该邮件从移动设备发送 --原始邮件-- 发件人："Mark Abraham "; 发送时间：2018年8月13日(星期一) 晚上11:02 收件人："gmx-users" ; 抄送："gromacs.org_gmx-users "; 主题：Re: [gmx-users] Mixing rule between organic and inorganic units --- Hi, What experimental data can you replicate to show the model is valid? Mark On Mon, Aug 13, 2018, 17:34 Baolin Huang wrote: > Dear All, >I studied the interactions between BMP-2 (protein) and hydroxyapatite > (HAP, inorganic material) by GROMACS with the OPLS-AA force field. The > mixing rule was the Lorentz-Berthelot combination. A reviewer commented > that 'The interaction of organic molecule on inorganic material needs > careful treatment in classical MD simulation since it is well known that > the mixing rule does not work well.' >How to answer this comment? How to validate the mixing rule is suitable > to calculate the interaction between organic and inorganic units? > > > Best wishes, > > -- > > Dr. Baolin Huang > Lecturer, School of Life Sciences, Guangzhou University > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Mixing rule between organic and inorganic units
Dear All, I studied the interactions between BMP-2 (protein) and hydroxyapatite (HAP, inorganic material) by GROMACS with the OPLS-AA force field. The mixing rule was the Lorentz-Berthelot combination. A reviewer commented that 'The interaction of organic molecule on inorganic material needs careful treatment in classical MD simulation since it is well known that the mixing rule does not work well.' How to answer this comment? How to validate the mixing rule is suitable to calculate the interaction between organic and inorganic units? Best wishes, -- Dr. Baolin Huang Lecturer, School of Life Sciences, Guangzhou University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] No default Ryckaert-Bell. types
Dear All, I experienced an error as follows: (I used the OPLS-AA force field) ERROR 48600 [file topol_Other_chain_C.itp, line 144934]: No default Ryckaert-Bell. types Anyone can help? Kind regards, -- Dr. Baolin Huang Lecturer, School of Life Sciences, Guangzhou University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Cannot find position restraint restraint.gro
Well done. Thanks for your help. -- Dr. Baolin Huang Lecturer, School of Life Sciences, Guangzhou University Guangzhou 510006, P.R. China -- Original -- From: "Alex"; Date: Sun, Jul 1, 2018 03:11 PM To: "gmx-users"; Subject: Re: [gmx-users] Cannot find position restraint restraint.gro The error is self-explanatory: new versions require a set of coordinates to be used with restraints, i.e. when using grompp, you have to use -r to specify these coordinates in addition to -c. The error message even suggests the simplest solution: instead of -c stuff.pdb use -c stuff.pdb -r stuff.pdb Alex On 7/1/2018 12:57 AM, Baolin Huang wrote: > Hi guys, > How to fix the problem as following: > Fatal error: > Cannot find position restraint file restraint.gro (option -r). > >From GROMACS-2018, you need to specify the position restraint coordinate > >files explicitly to avoid mistakes, although you can still use the same file > >as you specify for the -c option. > > Kind regards, > Baolin > > > > > > -- > > Dr. Baolin Huang > Lecturer, School of Life Sciences, Guangzhou University > Guangzhou 510006, P.R. China > Email:hb...@gzhu.edu.cn > Phone:+86-13917508029 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Cannot find position restraint restraint.gro
Hi guys, How to fix the problem as following: Fatal error: Cannot find position restraint file restraint.gro (option -r). >From GROMACS-2018, you need to specify the position restraint coordinate files >explicitly to avoid mistakes, although you can still use the same file as you >specify for the -c option. Kind regards, Baolin -- Dr. Baolin Huang Lecturer, School of Life Sciences, Guangzhou University Guangzhou 510006, P.R. China Email:hb...@gzhu.edu.cn Phone:+86-13917508029 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Core Dump
Hi All, I am using GRMACS 5.0.4, I got and error: Core dump on signal SIGBUS (7) suppressed. There was a warning: This run will generate roughly 3298 Mb of data. Kind regards, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Core Dump
Hi, Thanks for help. It was not grommp fault. The command line was mdrun_mpi -ntomp 1 -s relaxation.tp -deffnm relaxation -c HAP_relaxation.pdb Hope following can help. MPT: On host cl2n109, Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 0, Process 220661: Dumping core on signal SIGBUS(7) into directory /home/huangb2/test MPT: Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 1, Process 220662: Core dump on signal SIGBUS(7) suppressed. MPT: Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 2, Process 220663: Core dump on signal SIGBUS(7) suppressed. MPT: Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 3, Process 220664: Core dump on signal SIGBUS(7) suppressed. MPT: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize() aborting job MPT: Received signal 7 Kind regards, Alex -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Thursday, 19 March 2015 10:05 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Core Dump On 3/18/15 7:48 PM, BAOLIN HUANG wrote: Hi All, I am using GRMACS 5.0.4, I got and error: Core dump on signal SIGBUS (7) suppressed. There was a warning: This run will generate roughly 3298 Mb of data. So grompp seg faults? You're going to have to provide real information, like what your command was, relevant output, etc. There's nothing that can be diagnosed here. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] KALP-15 in DPPC tutorial
Hi All, I am doing the GROMACS Tutorial of KALP-15 in DPPC. Now, I get stuck at Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called confout.gro): perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat The command line was gmx grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr. And I got Fatal error: number of coordinates in coordinate file (system_inflated.gro, 6438) does not match topology (topol.top 888444) I tried to add DPPC 128 in the [ molecules ], however, I got Fatal error: No such moleculetype DPPC. How to update the [molecules] in topol.top? And how do I know the number of molecules? Kind regards, Alex Huang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
