Re: [gmx-users] Problem force constant bond stretc.
Den 2020-04-15 kl. 23:48, skrev Paolo Costa: Dear Gromacs users, I have a problem regarding force constant for bond stretching. By employing VFFDT software, I got C-C bond stretching force constant (for Benzene, B3LYP-6311++G*) equal to 383.23 kcal/ (mol A^2) which is equivalent to 160343 kj/ (mol nm^2). However when I look to the ffbonded.itp file of Amber99.ff the CA-CA force constant value is 392459.2 kj/ (mol nm^2). It seems that the value I got from VFFDT is somehow half than the one reported in Amber force field. Can somebody help me to figure out such issue? Thanks a lot in advance for your help. Vbond = (k/2) (r - r0)^2 Some methods do not use the division by two, so it can be a matter of definition. -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.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] Problem force constant bond stretc.
Dear Gromacs users, I have a problem regarding force constant for bond stretching. By employing VFFDT software, I got C-C bond stretching force constant (for Benzene, B3LYP-6311++G*) equal to 383.23 kcal/ (mol A^2) which is equivalent to 160343 kj/ (mol nm^2). However when I look to the ffbonded.itp file of Amber99.ff the CA-CA force constant value is 392459.2 kj/ (mol nm^2). It seems that the value I got from VFFDT is somehow half than the one reported in Amber force field. Can somebody help me to figure out such issue? Thanks a lot in advance for your help. -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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] (NEW USER) Determining Complex Dielectric property of a solid state system
Den 2020-04-15 kl. 13:30, skrev Tahsin Ashraf Khan: Hi All Hope everyone is doing well. I'm Tahsin, currently doing a Master of Engineering in Electronics at Macquarie University, Sydney, Australia. I would like to request everyone here to shed some light regarding a research I'm currently involved in. We are trying to develop a method of determining the Complex Dielectric property of solid sate systems through MD simulations. We've chosen the GROMACS software package to do that. Similar works have been done before but all of them involved solution-based systems. To be honest, It's been just 2 months that I'm trying to learn MD simulations so I'm not at all well versed in the capabilities of GROMACS. Have a nice day. Best Regards Tahsin Have you done your simulations and run gmx dipoles to analyze? And then gmx dielectric on the output of that? Please report back when you have, this is a bit tricky business though. You may check my old paper, however it is not entirely correct since trying to extract the dielectric constant at infinite frequency from a non-polarizable ff is not possible. https://aip.scitation.org/doi/abs/10.1063/1.476482 -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.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] Can we implement NMR restraint data in Gromacs?
Den 2020-04-15 kl. 14:15, skrev Chaturvedi Navneet: Dear GMX user, I am working on NEF (NMR Exchange Format). I need to use NMR restraint data in gromacs (in force field) for simulation. Does Gromacs support either reading or writing NEF format at the moment? If yes, then how can we implement NMR restrain data like dihedral, angle, chemical shifts, NOE restrains with Gromacs associated force field? If not, which machine can I go for simulation using these data? Many thanks We are working on an importer for NMR star files. Would that help? Please contact me off the mailing list in that case. -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.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] Error with Output from GMX cluster analysis
Dear GMX users, I am currently trying to use GMX to perform cluster analysis on a polymer. Inside the top file, I have two polymer molecules. After using the GMX cluster size, I got the following error. Kindly help with possible correction (if any) for this anomaly. Thank you Regards, Teslim Command line: gmx_mpi clustsize -f ../HPAM50_16%G_20%H_agg.nojump.mol.xtc -n polymer.ndx -s polymer.tpr -mol yes -cut 0.35 -pbc yes Reading frame 0 time 200.000 Reading file polymer.tpr, VERSION 2018.1 (single precision) Reading file polymer.tpr, VERSION 2018.1 (single precision) Using molecules rather than atoms. Not reading index file polymer.ndx Last frame 2 time 200200.000 Total number of atoms in clusters = 1 cmid: 1, cmax: 2, max_size: 2 cmid: 2, cmax: 2, max_size: 2 --- Program: gmx clustsize, version 2018.1 Source file: src/gromacs/fileio/matio.cpp (line 681) Fatal error: Lo: 0.00, Mid: 2.00, Hi: 2.00 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -- 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] Can we implement NMR restraint data in Gromacs?
Dear GMX user, I am working on NEF (NMR Exchange Format). I need to use NMR restraint data in gromacs (in force field) for simulation. Does Gromacs support either reading or writing NEF format at the moment? If yes, then how can we implement NMR restrain data like dihedral, angle, chemical shifts, NOE restrains with Gromacs associated force field? If not, which machine can I go for simulation using these data? Many thanks -- *Navaneet Chaturvedi* University of Leicester, UK Email: nc...@leicester.ac.uk -- 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] semiisotropic pressure coupling.
Incredible thank you. On Wed., 15 Apr. 2020, 8:46 pm Justin Lemkul, wrote: > > > On 4/14/20 10:12 PM, Miro Astore wrote: > > Hello all, > > > > I am working with a rather large membrane bound protein. I was getting > > an issue awhile ago where if the protein moved to the edge of the box > > the box would elongate in the z direction. I fixed this in the short > > term by setting my xy compressibility to 0 in my production mdp file > > pcoupl = Parrinello-Rahman > > pcoupltype = semiisotropic > > tau_p = 5.0 > > > > compressibility = 0 4.5e-5 > > ref_p = 1.0 1.0 > > compressibility = 0 4.5e-5 > > ref_p = 1.0 1.0 > > > > I have a few questions, why was it blowing up in the first place? I > > This was due to a CHARMM-specific bug in which CMAP forces were not > correctly calculated when two atoms were in different periodic images: > > http://manual.gromacs.org/current/release-notes/2019/2019.4.html#fix-incorrect-pressure-when-atoms-in-cmap-cross-a-box-boundary > > It was fixed in version 2019.4. > > Update your GROMACS version and you don't have to try playing any tricks > like zero compressibility. > > -Justin > > > would guess its to do with how the pressure is being calculated when > > this large 'vacuum' is being created in the solvent when the protein > > wraps around since my tc_grps is Protein non-Protein. The fact the > > problem only occurs when the protein wraps seems to indicate this sort > > of artifact, I can get into the hundreds of nano seconds before the > > protein drifts if I'm lucky, this is all after a well equilibrated > > system. > > > > I could fix the protein in the center of the box but I fear that might > > produce artifacts and I suspect there is a better way. > > > > I want to start studying how this protein interacts with the lipids > > and fixing the xy box size is not conducive to this so I'm wondering > > how I can let the lipids fluctuate while still maintaining sensible > > system behavior. > > > > Thank you for your time, > > > > Best, Miro > > > > mdp file can be found at > > > https://docs.google.com/document/d/16vsS4OOco9U3bUkarzSduN2OXohnBVVLedwLJanUi4w/edit?usp=sharing > > -- > > Miro A. Astore (he/him) > > PhD Candidate | Computational Biophysics > > Office 434 A28 School of Physics > > University of Sydney > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 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] (NEW USER) Determining Complex Dielectric property of a solid state system
Hi All Hope everyone is doing well. I'm Tahsin, currently doing a Master of Engineering in Electronics at Macquarie University, Sydney, Australia. I would like to request everyone here to shed some light regarding a research I'm currently involved in. We are trying to develop a method of determining the Complex Dielectric property of solid sate systems through MD simulations. We've chosen the GROMACS software package to do that. Similar works have been done before but all of them involved solution-based systems. To be honest, It's been just 2 months that I'm trying to learn MD simulations so I'm not at all well versed in the capabilities of GROMACS. Have a nice day. Best Regards Tahsin -- 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] semiisotropic pressure coupling.
On 4/14/20 10:12 PM, Miro Astore wrote: Hello all, I am working with a rather large membrane bound protein. I was getting an issue awhile ago where if the protein moved to the edge of the box the box would elongate in the z direction. I fixed this in the short term by setting my xy compressibility to 0 in my production mdp file pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 compressibility = 0 4.5e-5 ref_p = 1.0 1.0 compressibility = 0 4.5e-5 ref_p = 1.0 1.0 I have a few questions, why was it blowing up in the first place? I This was due to a CHARMM-specific bug in which CMAP forces were not correctly calculated when two atoms were in different periodic images: http://manual.gromacs.org/current/release-notes/2019/2019.4.html#fix-incorrect-pressure-when-atoms-in-cmap-cross-a-box-boundary It was fixed in version 2019.4. Update your GROMACS version and you don't have to try playing any tricks like zero compressibility. -Justin would guess its to do with how the pressure is being calculated when this large 'vacuum' is being created in the solvent when the protein wraps around since my tc_grps is Protein non-Protein. The fact the problem only occurs when the protein wraps seems to indicate this sort of artifact, I can get into the hundreds of nano seconds before the protein drifts if I'm lucky, this is all after a well equilibrated system. I could fix the protein in the center of the box but I fear that might produce artifacts and I suspect there is a better way. I want to start studying how this protein interacts with the lipids and fixing the xy box size is not conducive to this so I'm wondering how I can let the lipids fluctuate while still maintaining sensible system behavior. Thank you for your time, Best, Miro mdp file can be found at https://docs.google.com/document/d/16vsS4OOco9U3bUkarzSduN2OXohnBVVLedwLJanUi4w/edit?usp=sharing -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 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.
