[gmx-users] source cord routines for electric fields
Dear Gromacs experts: I'd like to add the time-dependent function to the electric field routines in GROMACS. I could only found the input (reading) codes in src/kernel/readir.c. Does anyone know which source cord routines I should modify to add the time-dependent functions. Thank you for advance. Makoto Yoneya, Dr. AIST, Tsukuba JAPAN -- 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] source cord routines for electric fields
On 2014-10-02 08:01, 米谷慎 wrote: Dear Gromacs experts: I'd like to add the time-dependent function to the electric field routines in GROMACS. I could only found the input (reading) codes in src/kernel/readir.c. Does anyone know which source cord routines I should modify to add the time-dependent functions. Thank you for advance. Makoto Yoneya, Dr. AIST, Tsukuba JAPAN mdlib/sim_util.c look for function calc_f_el -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] source cord routines for electric fields
Dear David: Thank a lot for your quick reply. I'd found the code already includes some time-dependent function. I'll study how to use it. Thanks a lot again. Makoto Yoneya, Dr. AIST, Tsukuba JAPAN On 2014-10-02 08:01, 米谷慎 wrote: Dear Gromacs experts: I'd like to add the time-dependent function to the electric field routines in GROMACS. I could only found the input (reading) codes in src/kernel/readir.c. Does anyone know which source cord routines I should modify to add the time-dependent functions. Thank you for advance. Makoto Yoneya, Dr. AIST, Tsukuba JAPAN mdlib/sim_util.c look for function calc_f_el -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. -- 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] User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2
Dear all, I am a student in Physics at Milan University. For my thesis, I should run a simulation of a binary liquid mixture of Argon and Krypton. Until now, I have been learning how to use GROMACS (version 5.0.1 and, since yesterady, 5.0.2) essentials, and my simulations were all based on LJ potential, and all was fine. Now I want to use a tabulated potential, that is a more detailed potential, different in form from LJ, taken from literature. I followed the steps of the instructions on GROMACS website (http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential) and the attached pdf, but it doesn't work. I ought to use cutoff-scheme = verlet (because the group scheme does not make sense, because my system has no charge), but I receive these errors from grompp: ERROR 1 [file Aziz.mdp]: With Verlet lists only cut-off and PME LJ interactions are supported ERROR 2 [file Aziz.mdp]: With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported Aziz.mdp is my mdp file, that contains the instructions coulombtype = User and vdwtype = User. What am I missing? Or it is true that GROMACS is not able to use user-defined potentials with verlet's cutoff? This would be a serious handicap for this code! Am I forced to use charge groups? Thanks in advance, Francesco Mambretti - University of Milan - LCP (Parallel Computing Lab) -- 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] User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2
On 02.10.2014 11:58, Francesco Mambretti wrote: Or it is true that GROMACS is not able to use user-defined potentials with verlet's cutoff? This would be a serious handicap for this code! Am I forced to use charge groups? Please read this thread: https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg01273.html Looks like it will appear at some point in the future. I'd be very glad about that too. M. -- 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] User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2
On Thu, Oct 2, 2014 at 11:58 AM, Francesco Mambretti francesco.mambre...@studenti.unimi.it wrote: Dear all, I am a student in Physics at Milan University. For my thesis, I should run a simulation of a binary liquid mixture of Argon and Krypton. Until now, I have been learning how to use GROMACS (version 5.0.1 and, since yesterady, 5.0.2) essentials, and my simulations were all based on LJ potential, and all was fine. Now I want to use a tabulated potential, that is a more detailed potential, different in form from LJ, taken from literature. I followed the steps of the instructions on GROMACS website ( http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential ) and the attached pdf, but it doesn't work. I ought to use cutoff-scheme = verlet (because the group scheme does not make sense, because my system has no charge), VDW-only systems work fine in the group scheme, e.g. with a single atom per charge group - but you will need to organize your own details for adequate buffering. but I receive these errors from grompp: ERROR 1 [file Aziz.mdp]: With Verlet lists only cut-off and PME LJ interactions are supported ERROR 2 [file Aziz.mdp]: With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported Aziz.mdp is my mdp file, that contains the instructions coulombtype = User and vdwtype = User. What am I missing? Or it is true that GROMACS is not able to use user-defined potentials with verlet's cutoff? This would be a serious handicap for this code! Am I forced to use charge groups? For now, yes. There is work in progress to implement user tables for the Verlet scheme ( GPUs). Some help with alpha-stage testing would be very welcome! But for that, you might like to have a working group-scheme setup against which to validate. Mark Thanks in advance, Francesco Mambretti - University of Milan - LCP (Parallel Computing Lab) -- 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] R: Re: User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2
So then, you have to update the pages on your website (http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential) about tabulated potentials, and also in the user manual (5.0.1 version). Otherwise, people risks misleading about this topic! In fact, I spent my last month in learning GROMACS, encouraged by the documentation about tabulated potentials (it seems so easy to do that!), and nothing is said about the cutoff scheme you have to use! And also the attached pdf should be updated. This is a very strong limit, LJ and Buckingham potentials are often not so accurate potentials, if you really want to simulate physical systems. So the alternatives I have are: 1) use group charge (e.g.: I have 108 atoms of mixed Ar and Kr, and each of them is a group charge) and group cutoff - but the run will require more time 2) downgrade my GROMACS version, so that I am not forced to use verlet cutoff if I want a configuration that scales fast 3) use LJ potential Am I right? Francesco Il 02/10/14, Mark Abraham mark.j.abra...@gmail.com ha scritto: On Thu, Oct 2, 2014 at 11:58 AM, Francesco Mambretti francesco.mambre...@studenti.unimi.it wrote: Dear all, I am a student in Physics at Milan University. For my thesis, I should run a simulation of a binary liquid mixture of Argon and Krypton. Until now, I have been learning how to use GROMACS (version 5.0.1 and, since yesterady, 5.0.2) essentials, and my simulations were all based on LJ potential, and all was fine. Now I want to use a tabulated potential, that is a more detailed potential, different in form from LJ, taken from literature. I followed the steps of the instructions on GROMACS website ( http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential ) and the attached pdf, but it doesn't work. I ought to use cutoff-scheme = verlet (because the group scheme does not make sense, because my system has no charge), VDW-only systems work fine in the group scheme, e.g. with a single atom per charge group - but you will need to organize your own details for adequate buffering. but I receive these errors from grompp: ERROR 1 [file Aziz.mdp]: With Verlet lists only cut-off and PME LJ interactions are supported ERROR 2 [file Aziz.mdp]: With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported Aziz.mdp is my mdp file, that contains the instructions coulombtype = User and vdwtype = User. What am I missing? Or it is true that GROMACS is not able to use user-defined potentials with verlet's cutoff? This would be a serious handicap for this code! Am I forced to use charge groups? For now, yes. There is work in progress to implement user tables for the Verlet scheme ( GPUs). Some help with alpha-stage testing would be very welcome! But for that, you might like to have a working group-scheme setup against which to validate. Mark Thanks in advance, Francesco Mambretti - University of Milan - LCP (Parallel Computing Lab) -- 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.
Re: [gmx-users] R: Re: User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2
On Thu, Oct 2, 2014 at 1:13 PM, Francesco Mambretti francesco.mambre...@studenti.unimi.it wrote: So then, you have to update the pages on your website ( http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential) about tabulated potentials, Indeed, I have fixed that. Unfortunately, much of the Gromacs documentation precedes the existence of the Verlet scheme, and we have not made a systematic attempt to update all of it. and also in the user manual (5.0.1 version). Noted Otherwise, people risks misleading about this topic! In fact, I spent my last month in learning GROMACS, encouraged by the documentation about tabulated potentials (it seems so easy to do that!), and nothing is said about the cutoff scheme you have to use! And also the attached pdf should be updated. That would be up to the user who contributed it, unfortunately. This is a very strong limit, LJ and Buckingham potentials are often not so accurate potentials, if you really want to simulate physical systems. So the alternatives I have are: 1) use group charge (e.g.: I have 108 atoms of mixed Ar and Kr, and each of them is a group charge) and group cutoff - but the run will require more time I'd expect that a tiny VDW-only system like that will show little to no performance difference between the cutoff schemes (assuming the group scheme setup is buffered), because both make about the same use of SIMD intrinsics and the effect spent in optimizing for your kind of systems is about the same in both. Once tables work in Verlet, I'd expect even less difference between the two (but GPU support will be great for larger systems). 2) downgrade my GROMACS version, so that I am not forced to use verlet cutoff if I want a configuration that scales fast You're not forced to use Verlet now ;-) The default scheme changed in 5, but the group scheme is still there (and works better than ever). There's zero value in using an earlier version. Mark 3) use LJ potential Am I right? Francesco Il 02/10/14, Mark Abraham mark.j.abra...@gmail.com ha scritto: On Thu, Oct 2, 2014 at 11:58 AM, Francesco Mambretti francesco.mambre...@studenti.unimi.it wrote: Dear all, I am a student in Physics at Milan University. For my thesis, I should run a simulation of a binary liquid mixture of Argon and Krypton. Until now, I have been learning how to use GROMACS (version 5.0.1 and, since yesterady, 5.0.2) essentials, and my simulations were all based on LJ potential, and all was fine. Now I want to use a tabulated potential, that is a more detailed potential, different in form from LJ, taken from literature. I followed the steps of the instructions on GROMACS website ( http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential ) and the attached pdf, but it doesn't work. I ought to use cutoff-scheme = verlet (because the group scheme does not make sense, because my system has no charge), VDW-only systems work fine in the group scheme, e.g. with a single atom per charge group - but you will need to organize your own details for adequate buffering. but I receive these errors from grompp: ERROR 1 [file Aziz.mdp]: With Verlet lists only cut-off and PME LJ interactions are supported ERROR 2 [file Aziz.mdp]: With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported Aziz.mdp is my mdp file, that contains the instructions coulombtype = User and vdwtype = User. What am I missing? Or it is true that GROMACS is not able to use user-defined potentials with verlet's cutoff? This would be a serious handicap for this code! Am I forced to use charge groups? For now, yes. There is work in progress to implement user tables for the Verlet scheme ( GPUs). Some help with alpha-stage testing would be very welcome! But for that, you might like to have a working group-scheme setup against which to validate. Mark Thanks in advance, Francesco Mambretti - University of Milan - LCP (Parallel Computing Lab) -- 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 *
[gmx-users] Running jobs between different Gromacs versions
Hi, I was wondering if it is correct to prepare a Gromacs simulation with Gromacs 4.5.5 until production run and to do the production (starting from final tpr file) with Gromacs 5.0. Thanks in advance, Mustafa Tekpinar -- 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] Running jobs between different Gromacs versions
On 2014-10-02 14:00, Mustafa TEKPINAR wrote: Hi, I was wondering if it is correct to prepare a Gromacs simulation with Gromacs 4.5.5 until production run and to do the production (starting from final tpr file) with Gromacs 5.0. Thanks in advance, Mustafa Tekpinar Do another minimization with 5.0 before production, then you can say you have minimized the starting structure and run production with the same software. Be sure to upgrade to 5.0.2! -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Force field for phosphoserine
Hello everyone,Has anyone subjected a polypeptide containing a phosphoserine residue to :~$ pdb pdb2gmx ? The program does not recognize serine as it has a phosphorus atom attached to it which is not present in the definition. I am trying to define phosphoserine as a residue (let's say PSER). Can anyone tell me what all files do I need to edit (what kind of data do I need to look for, to be more specific) in order to make the program recognize this new residue ?Thanks in advance for help.Regards,Ashish Bihani -- 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] regarding GROMACS Tutorial KALP15 in DPPC
Thanks Justin I m running the command mdrun -s em.tpr and I did get the confout.gro file as output. after that I am running the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat and then again the energy minimization command. mdrun -s em.tpr After that I am solvating the system. I did put a local copy of vdwradii.dat in my working directorie and change the value of C from 0.15 to 0.375. I am solvating my system by the command genbox -cp system_shrink1.gro -cs spc216.gro -o system_solv.gro -p topol.top after that I am adding the ions in the system by the command grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But now I am getting an error number of coordinates in coordinate file (system_solv.gro, 8218) does not match topology (topol.top, 1956) can you please help what caused this error. Thanking you On Tue, Sep 30, 2014 at 8:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 10:30 AM, Anurag Dobhal wrote: Dear justin Thank you for your rely and precious time. I am aware that .gro file is to be visualized in VMD and its content can be checked in text editor. all the previous .gro file are visualized and checked in VMD. I have obetained that ( confout.gro )file by running the command of energy minimization i.e. mdrun -v -deffnm em and before this command I ran the command perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat after running the energy minimization the confout.gro is actually obetained as confout.gro.trr. so I am renaming it as confout.gro. so it is actually .trr format, which can not be visualised in VMD or checked in text editor. Which means it's an invalid input file format and that's why you're getting a failure from InflateGRO. If file names are given different extensions, you can't just randomly change them and expect things to work. If you ran mdrun -v -deffnm em you will never get anything named confout.gro. Note that the tutorial explicitly says: 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 You didn't use default names. You told mdrun name all of my files em.* when you invoked -deffnm. If you simply ran: mdrun -s em.tpr you would get confout.gro. In any case, you should have em.gro which is what you should use to proceed. I have no idea where confout.gro.trr came from, but it's a trajectory and clearly not what needs to be used 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 601 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. -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] parachem GMX
Dear all, I have used parachem to generate the topology file in .str format. Since I would like to use it in GROMACS software, I wonder how I can convert it to CHARMM force field format in GROMACS. Thanks, Yao -- 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] R: Re: R: Re: User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2
Ok thank you. Another question. 108 particles was just a test for beginning, but we would like to study much bigger systems (from 1000 to 1 particles at least). Is it possible and reasonable with the group scheme? Does it support parallel computing? Francesco Il 02/10/14 13:43, Mark Abraham mark.j.abra...@gmail.com ha scritto: On Thu, Oct 2, 2014 at 1:13 PM, Francesco Mambretti francesco.mambre...@studenti.unimi.it wrote: So then, you have to update the pages on your website ( http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential) about tabulated potentials, Indeed, I have fixed that. Unfortunately, much of the Gromacs documentation precedes the existence of the Verlet scheme, and we have not made a systematic attempt to update all of it. and also in the user manual (5.0.1 version). Noted Otherwise, people risks misleading about this topic! In fact, I spent my last month in learning GROMACS, encouraged by the documentation about tabulated potentials (it seems so easy to do that!), and nothing is said about the cutoff scheme you have to use! And also the attached pdf should be updated. That would be up to the user who contributed it, unfortunately. This is a very strong limit, LJ and Buckingham potentials are often not so accurate potentials, if you really want to simulate physical systems. So the alternatives I have are: 1) use group charge (e.g.: I have 108 atoms of mixed Ar and Kr, and each of them is a group charge) and group cutoff - but the run will require more time I'd expect that a tiny VDW-only system like that will show little to no performance difference between the cutoff schemes (assuming the group scheme setup is buffered), because both make about the same use of SIMD intrinsics and the effect spent in optimizing for your kind of systems is about the same in both. Once tables work in Verlet, I'd expect even less difference between the two (but GPU support will be great for larger systems). 2) downgrade my GROMACS version, so that I am not forced to use verlet cutoff if I want a configuration that scales fast You're not forced to use Verlet now ;-) The default scheme changed in 5, but the group scheme is still there (and works better than ever). There's zero value in using an earlier version. Mark 3) use LJ potential Am I right? Francesco Il 02/10/14, Mark Abraham mark.j.abra...@gmail.com ha scritto: On Thu, Oct 2, 2014 at 11:58 AM, Francesco Mambretti francesco.mambre...@studenti.unimi.it wrote: Dear all, I am a student in Physics at Milan University. For my thesis, I should run a simulation of a binary liquid mixture of Argon and Krypton. Until now, I have been learning how to use GROMACS (version 5.0.1 and, since yesterady, 5.0.2) essentials, and my simulations were all based on LJ potential, and all was fine. Now I want to use a tabulated potential, that is a more detailed potential, different in form from LJ, taken from literature. I followed the steps of the instructions on GROMACS website ( http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential ) and the attached pdf, but it doesn't work. I ought to use cutoff-scheme = verlet (because the group scheme does not make sense, because my system has no charge), VDW-only systems work fine in the group scheme, e.g. with a single atom per charge group - but you will need to organize your own details for adequate buffering. but I receive these errors from grompp: ERROR 1 [file Aziz.mdp]: With Verlet lists only cut-off and PME LJ interactions are supported ERROR 2 [file Aziz.mdp]: With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported Aziz.mdp is my mdp file, that contains the instructions coulombtype = User and vdwtype = User. What am I missing? Or it is true that GROMACS is not able to use user-defined potentials with verlet's cutoff? This would be a serious handicap for this code! Am I forced to use charge groups? For now, yes. There is work in progress to implement user tables for the Verlet scheme ( GPUs). Some help with alpha-stage testing would be very welcome! But for that, you might like to have a working group-scheme setup against which to validate. Mark Thanks in advance, Francesco Mambretti - University of Milan - LCP (Parallel Computing Lab) -- 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
Re: [gmx-users] R: Re: R: Re: User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2
On Thu, Oct 2, 2014 at 3:24 PM, Francesco Mambretti francesco.mambre...@studenti.unimi.it wrote: Ok thank you. Another question. 108 particles was just a test for beginning, but we would like to study much bigger systems (from 1000 to 1 particles at least). Is it possible and reasonable with the group scheme? Does it support parallel computing? Sure, for the last 15 years. :-) The group scheme has only MPI support (no OpenMP, no CUDA), so in practice you're limited to something like at least 500 atoms per rank(=core). YMMV because we don't study the performance on such systems. Mark Francesco Il 02/10/14 13:43, Mark Abraham mark.j.abra...@gmail.com ha scritto: On Thu, Oct 2, 2014 at 1:13 PM, Francesco Mambretti francesco.mambre...@studenti.unimi.it wrote: So then, you have to update the pages on your website ( http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential ) about tabulated potentials, Indeed, I have fixed that. Unfortunately, much of the Gromacs documentation precedes the existence of the Verlet scheme, and we have not made a systematic attempt to update all of it. and also in the user manual (5.0.1 version). Noted Otherwise, people risks misleading about this topic! In fact, I spent my last month in learning GROMACS, encouraged by the documentation about tabulated potentials (it seems so easy to do that!), and nothing is said about the cutoff scheme you have to use! And also the attached pdf should be updated. That would be up to the user who contributed it, unfortunately. This is a very strong limit, LJ and Buckingham potentials are often not so accurate potentials, if you really want to simulate physical systems. So the alternatives I have are: 1) use group charge (e.g.: I have 108 atoms of mixed Ar and Kr, and each of them is a group charge) and group cutoff - but the run will require more time I'd expect that a tiny VDW-only system like that will show little to no performance difference between the cutoff schemes (assuming the group scheme setup is buffered), because both make about the same use of SIMD intrinsics and the effect spent in optimizing for your kind of systems is about the same in both. Once tables work in Verlet, I'd expect even less difference between the two (but GPU support will be great for larger systems). 2) downgrade my GROMACS version, so that I am not forced to use verlet cutoff if I want a configuration that scales fast You're not forced to use Verlet now ;-) The default scheme changed in 5, but the group scheme is still there (and works better than ever). There's zero value in using an earlier version. Mark 3) use LJ potential Am I right? Francesco Il 02/10/14, Mark Abraham mark.j.abra...@gmail.com ha scritto: On Thu, Oct 2, 2014 at 11:58 AM, Francesco Mambretti francesco.mambre...@studenti.unimi.it wrote: Dear all, I am a student in Physics at Milan University. For my thesis, I should run a simulation of a binary liquid mixture of Argon and Krypton. Until now, I have been learning how to use GROMACS (version 5.0.1 and, since yesterady, 5.0.2) essentials, and my simulations were all based on LJ potential, and all was fine. Now I want to use a tabulated potential, that is a more detailed potential, different in form from LJ, taken from literature. I followed the steps of the instructions on GROMACS website ( http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential ) and the attached pdf, but it doesn't work. I ought to use cutoff-scheme = verlet (because the group scheme does not make sense, because my system has no charge), VDW-only systems work fine in the group scheme, e.g. with a single atom per charge group - but you will need to organize your own details for adequate buffering. but I receive these errors from grompp: ERROR 1 [file Aziz.mdp]: With Verlet lists only cut-off and PME LJ interactions are supported ERROR 2 [file Aziz.mdp]: With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported Aziz.mdp is my mdp file, that contains the instructions coulombtype = User and vdwtype = User. What am I missing? Or it is true that GROMACS is not able to use user-defined potentials with verlet's cutoff? This would be a serious handicap for this code! Am I forced to use charge groups? For now, yes. There is work in progress to implement user tables for the Verlet scheme ( GPUs). Some help with alpha-stage testing would be very welcome! But for that, you might like to have a working group-scheme setup
Re: [gmx-users] Force field for phosphoserine
On 10/2/14 8:45 AM, ashish bihani wrote: Hello everyone,Has anyone subjected a polypeptide containing a phosphoserine residue to :~$ pdb pdb2gmx ? The program does not recognize serine as it has a phosphorus atom attached to it which is not present in the definition. I am trying to define phosphoserine as a residue (let's say PSER). Can anyone tell me what all files do I need to edit (what kind of data do I need to look for, to be more specific) in order to make the program recognize this new residue ?Thanks in advance for help.Regards,Ashish Bihani http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field Otherwise, find a force field that contains parameters already (most force fields use SEP as phosphoserine, not PSER). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
On 10/2/14 8:50 AM, Anurag Dobhal wrote: Thanks Justin I m running the command mdrun -s em.tpr and I did get the confout.gro file as output. after that I am running the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat and then again the energy minimization command. mdrun -s em.tpr After that I am solvating the system. I did put a local copy of vdwradii.dat in my working directorie and change the value of C from 0.15 to 0.375. I am solvating my system by the command genbox -cp system_shrink1.gro -cs spc216.gro -o system_solv.gro -p topol.top after that I am adding the ions in the system by the command grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But now I am getting an error number of coordinates in coordinate file (system_solv.gro, 8218) does not match topology (topol.top, 1956) can you please help what caused this error. Don't solvate the intermediate steps. It makes no physical sense. Only solvate when you have shrunk the system to an appropriate size based on APL. Regardless, the number of atoms in the system is way too small to be correct for the tutorial system. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
Re: [gmx-users] parachem GMX
On 10/2/14 9:21 AM, xy21hb wrote: Dear all, I have used parachem to generate the topology file in .str format. Since I would like to use it in GROMACS software, I wonder how I can convert it to CHARMM force field format in GROMACS. Use our converter: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
how will I get to know that the system have shrunken enough, and which file I need to solvate. On Thu, Oct 2, 2014 at 9:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/2/14 8:50 AM, Anurag Dobhal wrote: Thanks Justin I m running the command mdrun -s em.tpr and I did get the confout.gro file as output. after that I am running the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat and then again the energy minimization command. mdrun -s em.tpr After that I am solvating the system. I did put a local copy of vdwradii.dat in my working directorie and change the value of C from 0.15 to 0.375. I am solvating my system by the command genbox -cp system_shrink1.gro -cs spc216.gro -o system_solv.gro -p topol.top after that I am adding the ions in the system by the command grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But now I am getting an error number of coordinates in coordinate file (system_solv.gro, 8218) does not match topology (topol.top, 1956) can you please help what caused this error. Don't solvate the intermediate steps. It makes no physical sense. Only solvate when you have shrunk the system to an appropriate size based on APL. Regardless, the number of atoms in the system is way too small to be correct for the tutorial system. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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. -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] regarding GROMACS Tutorial KALP15 in DPPC
On 10/2/14 12:51 PM, Anurag Dobhal wrote: how will I get to know that the system have shrunken enough, and which file I need to solvate. This is stated in the tutorial. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
[gmx-users] g_rdf of differents proteins
Hello, I made the simulation of lisozime following the tutorial of Gromacs to then calculate the values of g_rdf. I also made one simulation of another protein using another box model. I would like to know if i could make a comparison of g_rdf values between this protein and lisozime or if it's possible to compare only the distribution profile. Thank you very much -- *Yara Pereira Cerceau Alves* Graduanda em Engenharia de Alimentos Bolsista PIBIC/CNPq Universidade Federal de Viçosa - UFV/MG +55 32 99751550 -- 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] Martini force field - coarse grained protein tutorials
Hello, I am also attempting to run Martini using version 5 and am getting the same two errors with an mdp file that worked (aside from warnings) on version 4.6.5. Does anyone have a solution to this problem? -David On Mon, Sep 15, 2014 at 3:37 AM, Sridhar Kumar Kannam srisri...@gmail.com wrote: Hi Tsjerk, Thank you. I missed those links. Now when I minimize the system (protein in vacuum) I am getting the following errors. I am using 5.0 version. ERROR 1 [file minimization-vaccum.mdp]: With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported ERROR 2 [file minimization-vaccum.mdp]: Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier. Can you please explain them ... Thanks again. On Mon, Sep 15, 2014 at 5:23 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Sridhar, Have you tried clicking on the .mdp file names in the commands, which are underlined and highlighted in blue? Seems to work for me. Cheers, Tsjerk On Sep 14, 2014 12:41 PM, Sridhar Kumar Kannam srisri...@gmail.com wrote: Hi All, I am a newbie to Gromacs and Martini force field. I begin with the tutorials - http://md.chem.rug.nl/cgmartini/index.php/proteins As this tutorial does not provide the .mdp files I have tried to built the .mdp files based on other Gromacs tutorials. But when I run the simulations I am getting different kinds of error. As I have not read the manual yet, its hard to debug the errors. Can someone please share the *mdp files to run this tutorial (Ubiquitin and HIV-Prtease) simulations. Thank you. -- Cheers !!! Sridhar Kumar Kannam :) -- 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. -- Cheers !!! Sridhar Kumar Kannam :) -- 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.
Re: [gmx-users] Martini force field - coarse grained protein tutorials
On 10/2/14 1:39 PM, David Ackerman wrote: Hello, I am also attempting to run Martini using version 5 and am getting the same two errors with an mdp file that worked (aside from warnings) on version 4.6.5. Does anyone have a solution to this problem? It's because the default cutoff scheme has changed. Since the .mdp file does not specify a cutoff-scheme, grompp assumes Verlet, so the options given in the .mdp file trigger errors. If you specify cutoff-scheme = group or otherwise change the settings to be compatible with Verlet, grompp should work. The equivalent options under Verlet are all described on manual.gromacs.org and in the PDF manual. -Justin On Mon, Sep 15, 2014 at 3:37 AM, Sridhar Kumar Kannam srisri...@gmail.com wrote: Hi Tsjerk, Thank you. I missed those links. Now when I minimize the system (protein in vacuum) I am getting the following errors. I am using 5.0 version. ERROR 1 [file minimization-vaccum.mdp]: With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported ERROR 2 [file minimization-vaccum.mdp]: Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier. Can you please explain them ... Thanks again. On Mon, Sep 15, 2014 at 5:23 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Sridhar, Have you tried clicking on the .mdp file names in the commands, which are underlined and highlighted in blue? Seems to work for me. Cheers, Tsjerk On Sep 14, 2014 12:41 PM, Sridhar Kumar Kannam srisri...@gmail.com wrote: Hi All, I am a newbie to Gromacs and Martini force field. I begin with the tutorials - http://md.chem.rug.nl/cgmartini/index.php/proteins As this tutorial does not provide the .mdp files I have tried to built the .mdp files based on other Gromacs tutorials. But when I run the simulations I am getting different kinds of error. As I have not read the manual yet, its hard to debug the errors. Can someone please share the *mdp files to run this tutorial (Ubiquitin and HIV-Prtease) simulations. Thank you. -- Cheers !!! Sridhar Kumar Kannam :) -- 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. -- Cheers !!! Sridhar Kumar Kannam :) -- 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. Ruth L. Kirschstein NRSA 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 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.
[gmx-users] NPT Equilibrium?
Hi. The system is a ~ 165 amino acid protein with a 7 amino acid substrate, in an about 9000 water rhombic dodecahedron water box. I used thermostat for the whole system. 1. minimization to force 100. 2. NVT with position restrain on protein 0.3 ns 3. NPT with position restrain on protein 4. 30 ns NPT without position restraint. Average Total Energy: -310151 Total-Drift: -98.7985 5. 0.06 ns NPT Average Total Energy: -310371 Total-Drift: 618.659 6. 59 ns NPT Average Total Energy: -310207 Total-Drift: 24.0559 7. 59.1 ns NPT Average Total Energy: -310204 Total-Drift: 25.1117 8. 30 ns NPT Average Total Energy: -310204 Total-Drift: -31.0966 9. 30 ns NPT Average Total Energy: -310210 Total-Drift: -29.4525 Average Pressure: 1.16985 Total-Drift: -0.0824936 Is this at equilibrium yet? The barostat set to 1 bar. -- 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] Running jobs between different Gromacs versions
Hey :) Energy minimization will destroy anything you have for temperature and pressure and you'll have to re-equilibrate the thermo/barostat. I would say that a short pre-production run with GMX5 production conditions would be sufficient (and therefor better) to bring the system from a GMX4 ensemble to the GMX5 ensemble, just in case there is a small difference between them. Just my two cents. Cheers, Tsjerk On Thu, Oct 2, 2014 at 2:24 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2014-10-02 14:00, Mustafa TEKPINAR wrote: Hi, I was wondering if it is correct to prepare a Gromacs simulation with Gromacs 4.5.5 until production run and to do the production (starting from final tpr file) with Gromacs 5.0. Thanks in advance, Mustafa Tekpinar Do another minimization with 5.0 before production, then you can say you have minimized the starting structure and run production with the same software. Be sure to upgrade to 5.0.2! -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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 subject)
Dear users, I conduct folding simulation, this is my trial project before I conduct my own one. I simulate small protein, 1CRN. The aim is that i can simulate folding from primary protein structure to a fully-folded 3rd structure. To create primary protein structure, I created 1CRN.pdb based on fasta sequence using swisspdbviewer, then i use it in gromacs. After some preparation, I had succesfully minimized the protein using steep depest minimization. The I did nvt equilibration. Warning and Error was occured: *WARNING: Listed nonbonded interaction between particles 206 and 207at distance 23490.299 which is larger than the table limit 151.000 nm.This is likely either a 1,4 interaction, or a listed interaction insidea smaller molecule you are decoupling during a free energy calculation.Since interactions at distances beyond the table cannot be computed,they are skipped until they are inside the table limit again. You willonly see this message once, even if it occurs for several interactions.IMPORTANT: This should not happen in a stable simulation, so there isprobably something wrong with your system. Only change the table-extensiondistance in the mdp file if you are really sure that is the reason.* warning disnt appear anymore after i increased the value of table-extension to very high. however there still error message in nvt equilibration so that i cant continoue to the next step. *GROMACS: gmx mdrun, VERSION 5.0Executable: /usr/local/gromacs/bin//gmxLibrary dir: /usr/local/gromacs/share/gromacs/topCommand line: mdrun -nt 2 -deffnm nvtBack Off! I just backed up nvt.log to ./#nvt.log.9#Reading file nvt.tpr, VERSION 5.0 (single precision)Changing nstlist from 10 to 40, rlist from 1 to 1Using 1 MPI threadUsing 2 OpenMP threads Back Off! I just backed up nvt.trr to ./#nvt.trr.9#Back Off! I just backed up nvt.edr to ./#nvt.edr.9#Back Off! I just backed up nvt.xvg to ./#nvt.xvg.9#starting mdrun 'Protein in water'5000 steps, 10.0 ps.Step 0, time 0 (ps) LINCS WARNINGrelative constraint deviation after LINCS:rms 125.551300, max 1177.774780 (between atoms 268 and 269)bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 118119 90.00.1090 0.1947 0.1090264265 90.0 0.1090 0.1967 0.1090268269 98.60.1090 128.4865 0.1090387388 90.00.1090 0.2040 0.1090Back Off! I just backed up step0b.pdb to ./#step0b.pdb.18#Back Off! I just backed up step0c.pdb to ./#step0c.pdb.18#Wrote pdb files with previous and current coordinatesStep 0, time 0 (ps) LINCS WARNINGrelative constraint deviation after LINCS:rms 124.010127, max 1163.317261 (between atoms 268 and 269)bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length118119 90.00.1090 0.1942 0.1090264265 90.00.1090 0.1964 0.1090 268269 90.00.1090 126.9106 0.1090387388 90.0 0.1090 0.2036 0.1090Back Off! I just backed up step0b.pdb to ./#step0b.pdb.19#Back Off! I just backed up step0c.pdb to ./#step0c.pdb.19#Wrote pdb files with previous and current coordinatesSegmentation fault: 11* Can anyone help? any suggestions are very much welcomed. Thank You -- 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] NPT Equilibrium?
Hi Johnny, Equilibrium in energy, maybe, but check individual energy components, rather than totals. Equilibrium in dynamics is for sure not reached yet. Cheers, Tsjerk On Oct 2, 2014 7:52 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. The system is a ~ 165 amino acid protein with a 7 amino acid substrate, in an about 9000 water rhombic dodecahedron water box. I used thermostat for the whole system. 1. minimization to force 100. 2. NVT with position restrain on protein 0.3 ns 3. NPT with position restrain on protein 4. 30 ns NPT without position restraint. Average Total Energy: -310151 Total-Drift: -98.7985 5. 0.06 ns NPT Average Total Energy: -310371 Total-Drift: 618.659 6. 59 ns NPT Average Total Energy: -310207 Total-Drift: 24.0559 7. 59.1 ns NPT Average Total Energy: -310204 Total-Drift: 25.1117 8. 30 ns NPT Average Total Energy: -310204 Total-Drift: -31.0966 9. 30 ns NPT Average Total Energy: -310210 Total-Drift: -29.4525 Average Pressure: 1.16985 Total-Drift: -0.0824936 Is this at equilibrium yet? The barostat set to 1 bar. -- 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.
Re: [gmx-users] (no subject)
Dear Ainun. It looks like your system is exploding. Check the input coordinates. Cheers Cesar El 03/10/2014 01:10, AINUN NIZAR M 0810710...@mail.ub.ac.id escribió: Dear users, I conduct folding simulation, this is my trial project before I conduct my own one. I simulate small protein, 1CRN. The aim is that i can simulate folding from primary protein structure to a fully-folded 3rd structure. To create primary protein structure, I created 1CRN.pdb based on fasta sequence using swisspdbviewer, then i use it in gromacs. After some preparation, I had succesfully minimized the protein using steep depest minimization. The I did nvt equilibration. Warning and Error was occured: *WARNING: Listed nonbonded interaction between particles 206 and 207at distance 23490.299 which is larger than the table limit 151.000 nm.This is likely either a 1,4 interaction, or a listed interaction insidea smaller molecule you are decoupling during a free energy calculation.Since interactions at distances beyond the table cannot be computed,they are skipped until they are inside the table limit again. You willonly see this message once, even if it occurs for several interactions.IMPORTANT: This should not happen in a stable simulation, so there isprobably something wrong with your system. Only change the table-extensiondistance in the mdp file if you are really sure that is the reason.* warning disnt appear anymore after i increased the value of table-extension to very high. however there still error message in nvt equilibration so that i cant continoue to the next step. *GROMACS: gmx mdrun, VERSION 5.0Executable: /usr/local/gromacs/bin//gmxLibrary dir: /usr/local/gromacs/share/gromacs/topCommand line: mdrun -nt 2 -deffnm nvtBack Off! I just backed up nvt.log to ./#nvt.log.9#Reading file nvt.tpr, VERSION 5.0 (single precision)Changing nstlist from 10 to 40, rlist from 1 to 1Using 1 MPI threadUsing 2 OpenMP threads Back Off! I just backed up nvt.trr to ./#nvt.trr.9#Back Off! I just backed up nvt.edr to ./#nvt.edr.9#Back Off! I just backed up nvt.xvg to ./#nvt.xvg.9#starting mdrun 'Protein in water'5000 steps, 10.0 ps.Step 0, time 0 (ps) LINCS WARNINGrelative constraint deviation after LINCS:rms 125.551300, max 1177.774780 (between atoms 268 and 269)bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 118119 90.00.1090 0.1947 0.1090264265 90.0 0.1090 0.1967 0.1090268269 98.60.1090 128.4865 0.1090387388 90.00.1090 0.2040 0.1090Back Off! I just backed up step0b.pdb to ./#step0b.pdb.18#Back Off! I just backed up step0c.pdb to ./#step0c.pdb.18#Wrote pdb files with previous and current coordinatesStep 0, time 0 (ps) LINCS WARNINGrelative constraint deviation after LINCS:rms 124.010127, max 1163.317261 (between atoms 268 and 269)bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length118119 90.00.1090 0.1942 0.1090264265 90.00.1090 0.1964 0.1090 268269 90.00.1090 126.9106 0.1090387388 90.0 0.1090 0.2036 0.1090Back Off! I just backed up step0b.pdb to ./#step0b.pdb.19#Back Off! I just backed up step0c.pdb to ./#step0c.pdb.19#Wrote pdb files with previous and current coordinatesSegmentation fault: 11* Can anyone help? any suggestions are very much welcomed. Thank You -- 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.
