Re: [gmx-users] Free volume variation during the simulation
Den 2020-05-06 kl. 10:21, skrev Mohamed Abdelaal: Yes I measured both, the density and the free volume using gromacs. Since the free volume changes with respect to time, shouldn’t the density also change with time ? What do you mean with "changes"? If the density is constant (with fluctuations) in an equilibrium NPT simulation then the free volume should fluctuate around an average as well. If you have a NVT simulation on the other hand, the total density is going to be constant, but if your system undergoes a phase change the freevolume will change. Thanks, Mohamed On Wed, May 6, 2020 at 08:23 David van der Spoel wrote: Den 2020-05-06 kl. 01:13, skrev Mohamed Abdelaal: Hello everybody, I have two fundamental questions please. I have measured the fee volume and I discovered that, the free volume changes with respect to the time during the production run (different value for each frame). However I have measured the density but the result does not change with respect to time. Shouldn't the density also changes with time if the free volume changes with time ? I also can't understand why the free volume changes with respect to the time, if the number of molecules and volume of box didn't change. Many Thanks, Mohamed This is due to atomic fluctuations, that is they overlap more or less depending on their distance, Did you use the freevolume tool in gromacs? It may also depend on whether each freevolume calculations is converged (-ninsert option). -- 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. -- 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] Free volume variation during the simulation
Den 2020-05-06 kl. 01:13, skrev Mohamed Abdelaal: Hello everybody, I have two fundamental questions please. I have measured the fee volume and I discovered that, the free volume changes with respect to the time during the production run (different value for each frame). However I have measured the density but the result does not change with respect to time. Shouldn't the density also changes with time if the free volume changes with time ? I also can't understand why the free volume changes with respect to the time, if the number of molecules and volume of box didn't change. Many Thanks, Mohamed This is due to atomic fluctuations, that is they overlap more or less depending on their distance, Did you use the freevolume tool in gromacs? It may also depend on whether each freevolume calculations is converged (-ninsert option). -- 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] Trouble with restrained dihedrals
Den 2020-04-16 kl. 08:56, skrev Marko Petrovic: Hello I'm trying to run an Energy Minimisation run while restraining phi and psi of the central alanine of an alanine dipeptide in vacuum. Hopefully it won't make a difference if I run a EM equilibration or other run for this error/concept since I am trying to create a script for creating/updating the necessary files for several different simulation runs. The error message: ERROR 1 [file cv_restraints.itp, line 3]: Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest. (after the function type). The .itp file contents: [ dihedral_restraints ] ; ai aj ak al type label phi dphi kfac power 5 7 915 1 1 -67.652 0 1 2 7 91517 1 159.806 0 1 2 Not sure where you have this format from but it should be ; ai aj ak al type phi dphi kfac Other possibly relevant file snippets: .mdp file define row (1st row): define= -DPOSRES_CV topol.top ifdef statement (last in file): #ifdef POSRES_CV #include "cv_restraints.itp" #endif I hope this is the info needed to easily see what I've done wrong. (Also info on how to interpret the error message would be nice, like which 5 parameters the software found and how it coun'ts parameters so I can get them to 3 or 6 if the problem is in the .utp file) With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology -- 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] 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.
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.
Re: [gmx-users] Post processing REMD simulation
Den 2020-04-12 kl. 08:36, skrev Mohammad Madani: Dear Prof. Van der Spoel Many thanks for your email. In fact, I want to predict the structure of one highly disorder protein. I ran my Remd simulation for 16ns per each replica. I Checked the trajectory file of one of the replica randomly but I did not see any significant change in comparison with my initial Structure. I asked question about this issue from one of the professor in MIT, he suggest me that because the structure is disordered it will be important to characterize the ensemble you get out, rather than a single structure. Now, I do not know what should I do with this. Could you please help me with this? When you say you don't see any changes, have you visually inspected all the final structures? Another thing you can try is concatenate the trajectories from the 10 or 20 lowest temperature and run clustering analysis. Unfortunately 16 ns is not very long because it takes time to change conformation. It is also far from certain that your temperature exchange worked over the whole range, that is that structures cycled from 300K to 500K and back. The demux.pl script in the gromacs distribution may help analyzing that if it still works. Many thanks On Sun, Apr 12, 2020 at 2:25 AM David van der Spoel wrote: *Message sent from a system outside of UConn.* Den 2020-04-12 kl. 05:40, skrev Mohammad Madani: Dear all, Hi. I have problems about the analysis of the REMD simulation. I run the remd for folding the protein. I have 191 replicas, the temperature range is 300K to 500K. I ran the simulation 16 ns for each replica. and the exchange rate is between 0.3-0.4. Now, I have one trr file and one log file for each replica in its temperature. I do not how can analysis these outputs. Could you please help me with this? What would you like to analyze? You will have to write a couple of scripts to plot potential energy as a function of T for instance. Many thanks. Mohammad -- 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. -- 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] Post processing REMD simulation
Den 2020-04-12 kl. 05:40, skrev Mohammad Madani: Dear all, Hi. I have problems about the analysis of the REMD simulation. I run the remd for folding the protein. I have 191 replicas, the temperature range is 300K to 500K. I ran the simulation 16 ns for each replica. and the exchange rate is between 0.3-0.4. Now, I have one trr file and one log file for each replica in its temperature. I do not how can analysis these outputs. Could you please help me with this? What would you like to analyze? You will have to write a couple of scripts to plot potential energy as a function of T for instance. Many thanks. Mohammad -- 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] Problem with pdb2gmx
Den 2020-04-11 kl. 11:38, skrev Elham Taghikhani: Hi Thank you for your response. I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it has warning in this case. As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. Give your ligand a different chain identifier such that gromacs knows these are different molecules. And make it a HETATM instead of ATOM. Thank you in advance Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 129 residues with 1971 atoms Chain time... Making bonds... Warning: Long Bond (1459-1462 = 0.259531 nm) Warning: Long Bond (1754-1757 = 0.259591 nm) Number of bonds was 1995, now 1995 Generating angles, dihedrals and pairs... Before cleaning: 5163 pairs Before cleaning: 5208 dihedrals Keeping all generated dihedrals Making cmap torsions... There are 5208 dihedrals, 429 impropers, 3556 angles 5127 pairs, 1995 bonds and 0 virtual sites Total mass 14324.281 a.m.u. Total charge 19.000 e Writing topology Processing chain 2 (39 atoms, 1 residues) Warning: Starting residue FLO1 in chain not identified as Protein/RNA/DNA. This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add FLO to residuetypes.dat if this was not correct. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 1 residues with 39 atoms Chain time... Making bonds... No bonds Generating angles, dihedrals and pairs... Making cmap torsions... There are 0 dihedrals, 0 impropers, 0 angles 0 pairs, 0 bonds and 0 virtual sites Total mass 373.322 a.m.u. Total charge 0.000 e Writing topology Including chain 1 in system: 1971 atoms 129 residues Including chain 2 in system: 39 atoms 1 residues Now there are 2010 atoms and 130 residues Total mass in system 14697.603 a.m.u. Total charge in system 19.000 e Writing coordinate file... - PLEASE NOTE You have successfully generated a topology from: complex.pdb. The Oplsaa force field and the spc water model are used. - ETON ESAELP On Saturday, April 11, 2020, 1:15:38 PM GMT+4:30, Elham Taghikhani wrote: Hi Thank you for your response. I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it doesn't work.As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. Thank you in advance. On Friday, April 10, 2020, 08:45:32 PM GMT+4:30, Elham Taghikhani wrote: Hi I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format. In the topology, I got this warning message : Warning:long-bond... I don't know what should I do to retain the covalent bond. I will appreciate it if you help me with this problem. -- 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] How to use GROMACS license?
Den 2020-04-04 kl. 16:18, skrev Nikhil Maroli: Dear GMX team, The GROMACS license allows one to use the codes inside a proprietary software? Basically, building a GUI and selling it for a higher price? Yes. As long as modifications to gromacs are available under the LGPL license as well. -- 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] Onsager coefficient
Den 2020-04-01 kl. 23:05, skrev Sina Omrani: Dear Mr Spoel, I have found out that I couldn't attach an image and I am sorry about that. here is a link to the picture. https://cdn1.imggmi.com/uploads/2020/4/1/1599cd9ac1102e329ff91759d3314725-full.png Not sure what is meant by r or v with two subscripts. Otherwise it looks a bit like Einsteins formula. On Tue, 31 Mar 2020 at 09:59, David van der Spoel wrote: Den 2020-03-30 kl. 22:51, skrev Sina Omrani: Hi dear Gromacs users, Sorry to ask again but I really appreciate the help on this subject. thanks. On Fri, 27 Mar 2020 at 02:23, Sina Omrani wrote: Hi, I would like to calculate the Onsager coefficient but after months of study, I'm not able to do that. if anybody can help me I would really appreciate it. I don't know if there is a specific command to do it or it needs a series of analyses. P.S. I attached a picture of a formula that calculates the Onsager coefficient from MD. sincerely, Sina Omrani I see no attachment and google does not help either. What is an Onsager coefficient? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- 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] Onsager coefficient
Den 2020-03-31 kl. 16:01, skrev Sina Omrani: it is Maxwell-Stefan. I want to calculate diffusion coefficients. from EMD we can calculate the MS diffusion coefficient that it is impossible to measure experimentally (because it is based on chemical potential gradient that is hard to measure) and with the thermodynamic correction factor it could be transformed into the Fick diffusion coefficient that is experimentally measurable. Although, there are NEMD method for calculating Fick diffusion coefficient but it is not prefered for some reasons. OK, thanks, interesting. This does not look too promising: https://en.wikipedia.org/wiki/Maxwell%E2%80%93Stefan_diffusion "A major disadvantage of the Maxwell–Stefan theory is that the diffusion coefficients, with the exception of the diffusion of dilute gases, do not correspond to the Fick's diffusion coefficients and are therefore not tabulated." Long time ago I published a paper about self-diffusion in alcohol-water mixtures as a function of concentration (J Chem Phys 119 (2003) p 7308). We mention "The relation between self diffusion and mutual diffusion is not straightforward58 and has hitherto only been studied by simulation for simple Lennard-Jones particles.59". But maybe this is not relevant at all. On Tue, 31 Mar 2020 at 17:51, David van der Spoel wrote: Den 2020-03-31 kl. 14:11, skrev Sina Omrani: As far as I know, the Onsager coefficient is used to calculate MS diffusion coefficient that is a microscopic property. Then we can use this MS coefficient and relate it to macroscopic properties that we already have experimentally. What does MS mean? And for my curiosity, what kind of macroscopic properties are you after? As far as I know many if not most macroscopic properties can be computed directly from a simulation, but I may be wrong. On Tue, 31 Mar 2020 at 11:05, David van der Spoel wrote: Den 2020-03-31 kl. 08:17, skrev Dallas Warren: 3.5.9 Onsager Relations https://www.iue.tuwien.ac.at/phd/mwagner/node44.html See 3.146 and 3.147 Thanks, I admit I am not familiar with this stuff, but seeing that this falls under the heading "Macroscopic Transport Models", what is the point in a microscopic simulation context? To prove or disprove or compare to the analytical relations? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 31 Mar 2020 at 16:28, David van der Spoel < sp...@xray.bmc.uu.se> wrote: Den 2020-03-30 kl. 22:51, skrev Sina Omrani: Hi dear Gromacs users, Sorry to ask again but I really appreciate the help on this subject. thanks. On Fri, 27 Mar 2020 at 02:23, Sina Omrani wrote: Hi, I would like to calculate the Onsager coefficient but after months of study, I'm not able to do that. if anybody can help me I would really appreciate it. I don't know if there is a specific command to do it or it needs a series of analyses. P.S. I attached a picture of a formula that calculates the Onsager coefficient from MD. sincerely, Sina Omrani I see no attachment and google does not help either. What is an Onsager coefficient? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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://ma
Re: [gmx-users] Onsager coefficient
Den 2020-03-31 kl. 14:11, skrev Sina Omrani: As far as I know, the Onsager coefficient is used to calculate MS diffusion coefficient that is a microscopic property. Then we can use this MS coefficient and relate it to macroscopic properties that we already have experimentally. What does MS mean? And for my curiosity, what kind of macroscopic properties are you after? As far as I know many if not most macroscopic properties can be computed directly from a simulation, but I may be wrong. On Tue, 31 Mar 2020 at 11:05, David van der Spoel wrote: Den 2020-03-31 kl. 08:17, skrev Dallas Warren: 3.5.9 Onsager Relations https://www.iue.tuwien.ac.at/phd/mwagner/node44.html See 3.146 and 3.147 Thanks, I admit I am not familiar with this stuff, but seeing that this falls under the heading "Macroscopic Transport Models", what is the point in a microscopic simulation context? To prove or disprove or compare to the analytical relations? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 31 Mar 2020 at 16:28, David van der Spoel wrote: Den 2020-03-30 kl. 22:51, skrev Sina Omrani: Hi dear Gromacs users, Sorry to ask again but I really appreciate the help on this subject. thanks. On Fri, 27 Mar 2020 at 02:23, Sina Omrani wrote: Hi, I would like to calculate the Onsager coefficient but after months of study, I'm not able to do that. if anybody can help me I would really appreciate it. I don't know if there is a specific command to do it or it needs a series of analyses. P.S. I attached a picture of a formula that calculates the Onsager coefficient from MD. sincerely, Sina Omrani I see no attachment and google does not help either. What is an Onsager coefficient? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Onsager coefficient
Den 2020-03-31 kl. 08:17, skrev Dallas Warren: 3.5.9 Onsager Relations https://www.iue.tuwien.ac.at/phd/mwagner/node44.html See 3.146 and 3.147 Thanks, I admit I am not familiar with this stuff, but seeing that this falls under the heading "Macroscopic Transport Models", what is the point in a microscopic simulation context? To prove or disprove or compare to the analytical relations? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 31 Mar 2020 at 16:28, David van der Spoel wrote: Den 2020-03-30 kl. 22:51, skrev Sina Omrani: Hi dear Gromacs users, Sorry to ask again but I really appreciate the help on this subject. thanks. On Fri, 27 Mar 2020 at 02:23, Sina Omrani wrote: Hi, I would like to calculate the Onsager coefficient but after months of study, I'm not able to do that. if anybody can help me I would really appreciate it. I don't know if there is a specific command to do it or it needs a series of analyses. P.S. I attached a picture of a formula that calculates the Onsager coefficient from MD. sincerely, Sina Omrani I see no attachment and google does not help either. What is an Onsager coefficient? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Onsager coefficient
Den 2020-03-30 kl. 22:51, skrev Sina Omrani: Hi dear Gromacs users, Sorry to ask again but I really appreciate the help on this subject. thanks. On Fri, 27 Mar 2020 at 02:23, Sina Omrani wrote: Hi, I would like to calculate the Onsager coefficient but after months of study, I'm not able to do that. if anybody can help me I would really appreciate it. I don't know if there is a specific command to do it or it needs a series of analyses. P.S. I attached a picture of a formula that calculates the Onsager coefficient from MD. sincerely, Sina Omrani I see no attachment and google does not help either. What is an Onsager coefficient? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Thin film drifting
Den 2020-03-29 kl. 22:46, skrev Alex: On Sun, Mar 29, 2020 at 2:49 PM David van der Spoel wrote: Den 2020-03-29 kl. 19:43, skrev Alex: Thanks. On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel < sp...@xray.bmc.uu.se> wrote: Den 2020-03-29 kl. 15:16, skrev Alex: Thank Prof. van der Spoel for the response. No, it isn't. The thin film is solid. There are interaction within the thin film and with water in the interface. Please find a short movie of the unwrapped trajectory of the simulation in below link (water molecules are hidden); It shows minimization, then equalization (NVT : tcoupl = v-rescale), then equalization (NpT : tcoupl = v-rescale and pcoupl = berendsen) and then production (NpT : tcoupl = v-rescale and pcoupl = Parrinello-Rahman). https://drive.google.com/open?id=1jk-Pun1BICNArGJaW0ydIY5TTivECGMf The thin film starts drifting significantly in the production along both x and y directions. Thanks, do you have isotropic pressure scaling? Yes, the pcoupltype is isotropic. Please find the mdp file in below link. https://drive.google.com/open?id=1iYt6eTcQ4SBi1A9ZFOenL7Q7wc37UvLa Is the shift towards higher x and y values? The shift is toward higher y value (+y). It also firstly goes toward higher x value (+x ) for a very short time and then switches the direction to toward lower x value (-x) and finally shifts toward lower x value (-x). But how is the solid modeled? Are there covalent bonds? It is not certain there is a problem, at least I am not convinced. In P scaling the coordinates of all particles are scaled by a constant and then certain atoms can hop over PBC. If you plot the center of mass including periodic boundaries (i.e. without unwrapping) it will be nicely in the center of the box with few fluctuations. gmx traj may do this for you. The thin film contains 1075 epoxy molecules in which there is no inter-molecule covalent bond. Below are the COM of the thin film with and without pbc in gmx traj. I admit you are right and the comm-grps works fine as gmx traj -pbc yes shows, thanks. PBC : Yes https://drive.google.com/open?id=14DRIZVt99x8SfO6qlkhPAeTkb7RQhsUp PBC: No https://drive.google.com/open?id=1uWRgTATW9hUEOaQQnQozklUvux8psrPx Note that the net movement is a lot smaller than the fluctuations in the in the one with PBC, I don't think there is any problem. I and many others have done PMFs of small compounds over membranes of different types, but not sure that anyone has noticed problems with moving membranes. I would also be so appreciated if you give me your preferences of the following two choices I have in the PMF calculation of Mol_A to the thin-film. “comm-grps = *thin_film* *Mol_A* *SOL*” or “comm-grps = *Other* *SOL*” Where the Other group contains the thin film and molecule A. I would go for comm-grps = system. Make sure to compute the pmf based on the relative distance between your compound and the membrane. Best regards, Alex Maybe you can open an issue here: https://gitlab.com/gromacs/gromacs/-/issues I will open an issue. Actually, in the later steps of the simulations, using umbrella sampling and wham, I want to simulate the PMF a single molecule (called A; 26 atoms) when it comes from water and diffuses inside the thin film till mid (com) of thin film. pull_group1 and pull_group2 would be the Mol_A and thin_film, respectively. I don't know if this kind of drifting would affect on the PMF, if so, how? If the comm-grps works I have the two following options to consider: “comm-grps = thin_film Mol_A SOL” or “comm-grps = Other SOL” Where the Other group contains the thin film and molecule A. Which one do you recommend, please? Thank you, Alex Best regards, Alex On Sun, Mar 29, 2020 at 2:44 AM David van der Spoel < sp...@xray.bmc.uu.se> wrote: Den 2020-03-29 kl. 05:24, skrev Alex: Dear all, In a system, I have a thin_film (infinitive in x-y directions) with water on top and bottom of it, PBC = xyz. By the below flags I try to remove the motion of the center of mass of the two group separately. comm-grps = thin_film Water comm-mode = Linear nstcomm = 100 However the thin film drift specially in x and y directions whereas I was expecting to have no drifting for the thin film, If I understood correctly the usage of the comm-grps! Would you please let me know how I can stop drifting of the thin film? Thank you, Alex Is that a liquid film? Are there interactions within the film and with water? The comm removal will calculate the center of mass taking periodic boundaries into account so if your film moves one molecule at a time the COM will stay in place. In a realistic system the friction between water and film should prevent this, hav eyou tried turning off comm? Historically this has been a fix for the Berendsen thermostat that accumulates energy, however with a stochastic thermostat it should not be necessary. Not sure about Nose-
Re: [gmx-users] Thin film drifting
Den 2020-03-29 kl. 19:43, skrev Alex: Thanks. On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel wrote: Den 2020-03-29 kl. 15:16, skrev Alex: Thank Prof. van der Spoel for the response. No, it isn't. The thin film is solid. There are interaction within the thin film and with water in the interface. Please find a short movie of the unwrapped trajectory of the simulation in below link (water molecules are hidden); It shows minimization, then equalization (NVT : tcoupl = v-rescale), then equalization (NpT : tcoupl = v-rescale and pcoupl = berendsen) and then production (NpT : tcoupl = v-rescale and pcoupl = Parrinello-Rahman). https://drive.google.com/open?id=1jk-Pun1BICNArGJaW0ydIY5TTivECGMf The thin film starts drifting significantly in the production along both x and y directions. Thanks, do you have isotropic pressure scaling? Yes, the pcoupltype is isotropic. Please find the mdp file in below link. https://drive.google.com/open?id=1iYt6eTcQ4SBi1A9ZFOenL7Q7wc37UvLa Is the shift towards higher x and y values? The shift is toward higher y value (+y). It also firstly goes toward higher x value (+x ) for a very short time and then switches the direction to toward lower x value (-x) and finally shifts toward lower x value (-x). But how is the solid modeled? Are there covalent bonds? It is not certain there is a problem, at least I am not convinced. In P scaling the coordinates of all particles are scaled by a constant and then certain atoms can hop over PBC. If you plot the center of mass including periodic boundaries (i.e. without unwrapping) it will be nicely in the center of the box with few fluctuations. gmx traj may do this for you. I and many others have done PMFs of small compounds over membranes of different types, but not sure that anyone has noticed problems with moving membranes. Maybe you can open an issue here: https://gitlab.com/gromacs/gromacs/-/issues I will open an issue. Actually, in the later steps of the simulations, using umbrella sampling and wham, I want to simulate the PMF a single molecule (called A; 26 atoms) when it comes from water and diffuses inside the thin film till mid (com) of thin film. pull_group1 and pull_group2 would be the Mol_A and thin_film, respectively. I don't know if this kind of drifting would affect on the PMF, if so, how? If the comm-grps works I have the two following options to consider: “comm-grps = thin_film Mol_A SOL” or “comm-grps = Other SOL” Where the Other group contains the thin film and molecule A. Which one do you recommend, please? Thank you, Alex Best regards, Alex On Sun, Mar 29, 2020 at 2:44 AM David van der Spoel < sp...@xray.bmc.uu.se> wrote: Den 2020-03-29 kl. 05:24, skrev Alex: Dear all, In a system, I have a thin_film (infinitive in x-y directions) with water on top and bottom of it, PBC = xyz. By the below flags I try to remove the motion of the center of mass of the two group separately. comm-grps = thin_film Water comm-mode = Linear nstcomm = 100 However the thin film drift specially in x and y directions whereas I was expecting to have no drifting for the thin film, If I understood correctly the usage of the comm-grps! Would you please let me know how I can stop drifting of the thin film? Thank you, Alex Is that a liquid film? Are there interactions within the film and with water? The comm removal will calculate the center of mass taking periodic boundaries into account so if your film moves one molecule at a time the COM will stay in place. In a realistic system the friction between water and film should prevent this, hav eyou tried turning off comm? Historically this has been a fix for the Berendsen thermostat that accumulates energy, however with a stochastic thermostat it should not be necessary. Not sure about Nose-Hoover though. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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
Re: [gmx-users] Thin film drifting
Den 2020-03-29 kl. 15:16, skrev Alex: Thank Prof. van der Spoel for the response. No, it isn't. The thin film is solid. There are interaction within the thin film and with water in the interface. Please find a short movie of the unwrapped trajectory of the simulation in below link (water molecules are hidden); It shows minimization, then equalization (NVT : tcoupl = v-rescale), then equalization (NpT : tcoupl = v-rescale and pcoupl = berendsen) and then production (NpT : tcoupl = v-rescale and pcoupl = Parrinello-Rahman). https://drive.google.com/open?id=1jk-Pun1BICNArGJaW0ydIY5TTivECGMf The thin film starts drifting significantly in the production along both x and y directions. Thanks, do you have isotropic pressure scaling? Is the shift towards higher x and y values? Maybe you can open an issue here: https://gitlab.com/gromacs/gromacs/-/issues Best regards, Alex On Sun, Mar 29, 2020 at 2:44 AM David van der Spoel wrote: Den 2020-03-29 kl. 05:24, skrev Alex: Dear all, In a system, I have a thin_film (infinitive in x-y directions) with water on top and bottom of it, PBC = xyz. By the below flags I try to remove the motion of the center of mass of the two group separately. comm-grps = thin_film Water comm-mode = Linear nstcomm = 100 However the thin film drift specially in x and y directions whereas I was expecting to have no drifting for the thin film, If I understood correctly the usage of the comm-grps! Would you please let me know how I can stop drifting of the thin film? Thank you, Alex Is that a liquid film? Are there interactions within the film and with water? The comm removal will calculate the center of mass taking periodic boundaries into account so if your film moves one molecule at a time the COM will stay in place. In a realistic system the friction between water and film should prevent this, hav eyou tried turning off comm? Historically this has been a fix for the Berendsen thermostat that accumulates energy, however with a stochastic thermostat it should not be necessary. Not sure about Nose-Hoover though. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Thin film drifting
Den 2020-03-29 kl. 05:24, skrev Alex: Dear all, In a system, I have a thin_film (infinitive in x-y directions) with water on top and bottom of it, PBC = xyz. By the below flags I try to remove the motion of the center of mass of the two group separately. comm-grps = thin_film Water comm-mode = Linear nstcomm = 100 However the thin film drift specially in x and y directions whereas I was expecting to have no drifting for the thin film, If I understood correctly the usage of the comm-grps! Would you please let me know how I can stop drifting of the thin film? Thank you, Alex Is that a liquid film? Are there interactions within the film and with water? The comm removal will calculate the center of mass taking periodic boundaries into account so if your film moves one molecule at a time the COM will stay in place. In a realistic system the friction between water and film should prevent this, hav eyou tried turning off comm? Historically this has been a fix for the Berendsen thermostat that accumulates energy, however with a stochastic thermostat it should not be necessary. Not sure about Nose-Hoover though. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Per atom energies
Den 2020-03-28 kl. 04:01, skrev Guilherme Carneiro Queiroz da Silva: Hi all, I look on google for any answers for such question in this maillist, and I found related questions but no final answer. I wish to compute the heat flux for my system using GK relations. I found the gromacs extension force the calculation of the per atom stress (http://www.mdstress.org/index.php/mdstresslib/). However, it still lacks the per atom energies. Did someone manage to extract such properties? I'm aware i could use enemat but had to do a large numbers of reruns in order to cover each atom obeying the group limit of gromacs, since this could be tedious I'm looking for other solutions. Could editing the trajectory code in order to extract not only forces but also the energies be the only solution? The reason that there is no support is that it is not physically meaningful, at least not to my knowledge. How would you partition the bond energy in a HCl molecule into atoms? In an isolated system it is in principle possible to compute interaction energies, using the typical pair potentials that classical force fields apply. However, these force fields ignore higher order interactions, which means this is a crude approximation. In a periodic system the computation of energies and energy components is even more cumbersome, although we have attempted that using potential of mean force calculation in JCTC 9 pp. 4542-4551 (2013). Thanks for any help, Guilherme Carneiro mdStress.org :: MDStressLib<http://www.mdstress.org/index.php/mdstresslib/> MDStress Library. MDStressLib is a standalone C++ library developed for local stress calculations. This library can be integrated into any molecular simulation code to compute local stress fields in 3D. www.mdstress.org -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] gmx msd unusual unit
Den 2020-03-16 kl. 15:10, skrev Justin Lemkul: On 3/16/20 10:07 AM, Joe Paul-Taylor wrote: Hello With running gmx msd I am told in the output the y axis unit is nm/ S2/ N, which is unexpected. Is this simply an print error or is there an error within the calculation? I have provided a copy of the output below, noting the units of the self-diffusion coefficient are sensible. Any insight would be much appreciated. The unit is correct. GROMACS does all distance calculations in terms of nm. You get an interpreted output of the MSD in traditional units for the diffusion constant. The confusion maybe about the xmgrace formatting :) nm^2 if you use the right software... -Justin # Created by: # :-) GROMACS - gmx msd, 2019.2 (-: # Command line: # gmx msd -s topol.tpr -f npt.xtc -b 3000 -e 13000 -o msd_IRMOF-NHPr_3OCT_8_run_1.xvg # gmx msd is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @ title "Mean Square Displacement" @ xaxis label "Time (ps)" @ yaxis label "MSD (nm\S2\N)" @TYPE xy # MSD gathered over 1 ps with 1001 restarts # Diffusion constants fitted from time 1000 to 9000 ps # D[ UNK] = 0.0031 (+/- 0.0004) (1e-5 cm^2/s) Thank you Joe -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] positive potential energy
Den 2020-03-15 kl. 20:53, skrev Afsane Farhadi: hi all I generated a box 4×4×4 (nm) with 100 molecules methyldiethanolamine by insert-molecules , forcefield is opls . after energy minimization the potential energy decreased but had a positive value . is my simulation wrong ? help me please Sent from Yahoo Mail on Android No. I just answered a similar question. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] potential energy doesn't have negative value
Den 2020-03-15 kl. 00:59, skrev Justin Lemkul: On 3/14/20 7:15 PM, Afsane Farhadi wrote: I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the potential energy is positive. the mdp file is attached. The mailing list does not accept attachments. ATB does produce GROMOS-compatible force fields, but it is always up to the user to determine if the parameters are suitable. A positive potential energy means that the intermolecular interactions are weak compared to the intramolecular (bonded) interactions. You can use gmx energy or look in the .log file to see the various contributions to the total potential energy. -Justin The baseline oof the potential energy is not a meaningful number in classical force fields. You have to subtract 100 times the energy of the monomer, then you will have the enthalpy of vaporization (+/- kT) which you can compare to experiment. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Setting a electric field in a simulation
Den 2020-03-10 kl. 03:17, skrev Mijiddorj B: Dear GMX users, I would like to perform MD simulations of solutions applying electric fields such as the microwave heating process. Is it possible to perform in gromacs? 1. How can I set the external electric field in the simulations? (from the user guide, I understood that I need to set 4 values electric-field-x = 2.0 150 5 0 How can I adjust the 2.45 GHz frequency? If you do not mind, please guide me. Best regards, Mijiddorj Why don't you try to play around and check the output file field.xvg to see what frequency you get? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Troubleshooting Generic Floating Point Exception Errors
Den 2020-03-09 kl. 20:14, skrev Travis Meyer: Hello all, I am a very new user to GROMACS and MD simulations in general. While going through some tutorials and other test simulations I've been getting some floating point exception errors. I recognize that there are a vast number of problems that could be causing this - I am not looking for any solutions to a specific problem, but am mostly wondering if there is a good procedure for troubleshooting these errors. Are there a couple of most-likely culprits which I should check first? Thanks in advance! Travis Travis Meyer, Ph.D. INSPIRE Postdoctoral Fellow Gormley Lab, Rutgers University These are rather uncommon unless you have truly unphysical setups (e.g. due to a unit problem) or broken hardware. Hard to tell based on your mail unfortunately. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Gromacs 2020 fails to run adh_cubic_vsites
Den 2020-03-07 kl. 17:04, skrev Rolly Ng: Dear Gromacs developers, I am new to Gromacs and I have recently compiled Gromacs 2020. I tried to run the ADH benchmarks from ftp://ftp.gromacs.org/pub/benchmarks/ADH_bench_systems.tar.gz The adh_cubic and adh_dodec completed successfully, but the adh_cubic_vsites and adh_dodec_vsites failed at grompp. Could you please have a look at the following output log? It actually tells you what is wrong in the input. -maxwarn 1 is your friend. Thanks, Rolly Ng PhD, Former Research Fellow, Department of Materials Science and Engineering City University of Hong Kong :-) GROMACS - gmx grompp, 2020-UNCHECKED (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca HamuraruVincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. LemkulViveca LindahlMagnus Lundborg Erik Marklund Pascal Merz Pieter MeulenhoffTeemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael ShirtsAlexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian WennbergMaarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2020-UNCHECKED Executable: /home/rolly/Gromacs/gromacs-2020/install/bin/gmx_mpi Data prefix: /home/rolly/Gromacs/gromacs-2020/install Working dir: /home/rolly/Gromacs/ADH_bench/adh_cubic_vsites Command line: gmx_mpi grompp -f pme_verlet_vsites.mdp -c conf.gro -p topol.top Ignoring obsolete mdp entry 'ns_type' Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' Setting the LD random seed to -1974193353 Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_B' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_C' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_D' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... WARNING 1 [file topol.top, line 55]: The following macros were defined in the 'define' mdp field with the -D prefix, but were not used in the topology: VSITE If you haven't made a spelling error, either use the macro you defined, or don't define the macro Cleaning up constraints and constant bonded interactions with virtual sites Removed 1683 Angles with virtual sites, 8136 left Removed 1587 Proper Dih.s with virtual sites, 16689 left Converted 2918 Constraints with virtual sites to connections, 2473 left Warning: removed 896 Constraints with vsite with Virtual site 3out construction This vsite construction does not guarantee constant bond-length If the constructions were generated by pdb2gmx ignore this warning Cleaning up constraints and constant bonded interactions with virtual sites Removed 1683 Angles with virtual sites, 8136 left Removed 1587 Proper Dih.s with virtual sites, 16689 left Converted 2918 Constraints with virtual sites to connections, 2473 left Warning: removed 896 Constraints with vsite with Virtual site 3out constru
Re: [gmx-users] Can't observe ion separation under the influence of electric field
Den 2020-02-12 kl. 23:07, skrev Live King: Dear all, I am running a simple test case with a lipid bilayer (DMPC), water, and ions (150mM KCL) under the influence of a constant electric field ( 300mV, 500mV, and 700mV). *I expected positive and negative ions to separate in the presence of an external electric field*. However, I am not observing such behavior despite running the all-atom simulation for 400ns in any case. I am using gromacs 2018.2, my mdp file is standard charmm-gui production with electric field option. for example 500mV electric field in Z-direction : electric-field-z = 0.060 0 0 0 ; *500**mv = 8.25nm* 0.060 = 500 mV * Are there any settings to run the electric field simulation that I miss? Any help will be greatly appreciated. Did you make density plots to check? Do you get an output field.xvg that prints the field strength? It may be optional though. The force on the atoms will be quite small still compared to interatomic forces therefore the effect may be limited. F = q E (convert to right units). In GROMACS MD units a typical interatomic force is ~ 1000 kJ/mol/nm^2. Thank you, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Estimation of configurational entropy
Den 2020-02-13 kl. 05:10, skrev Pathum Manjula Weerawarna: Hi everyone, I'm trying to estimate the configurational entropy of a small molecule using gmx anaeig. However, it does not allow me to use a mass-weighted covariance matrix for the calculation (only allow me to use mass-unweighted CV matrix). Theoretically, the use of a mass unweighted CV matrix for entropy calculation is inaccurate (frequencies going to be smaller). Does anybody know the accuracy of the entropy calculated using gmx anaeig? Also, is there any way to use a mass-weighted CV matrix for this calculation? The entropy is only the conformational entropy and can therefore be used for determining relative entropies, for instance for ligand binding (J Chem Theory Comput 9 pp. 4542-4551 (2013)). If you want to compute absolute entropies then for now normal mode analysis is the most efficient, even though it has limitations as well. See J Phys Chem A. 122 pp. 8982-8988 (2018). Sorry to promote my own papers but this is what I know :) Thank you so much for the help best Pathum Pathum M. Weerawarna, Ph.D. Postdoctoral Fellow Silverman Research Group Department of Chemistry Northwestern University 2145 Sheridan Road Evanston, IL 60208-3113 Phone: (316) 990-8542 Email : pathum.weerawa...@northwestern.edu pathumweerawa...@gmail.com [cid:1e2d5c51-a722-45d1-a750-8b9bf00f3e05]<https://www.linkedin.com/in/pathum-weerawarna-02384638/> -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Gromacs question
Den 2020-02-06 kl. 15:15, skrev Kneller, Daniel: Hi Dr. van der Spoel, I had hoped to reply using the user-lists but I realize now that I had the user-lists in digest mode and did not want to start another thread. CC-ing there anyway just such that it gets archived. Thank you for responding to my question about using gmx dos and the vibrational power spectrum option for gmx velacc for protein. I am interested in quantifying only the vibrational frequency of protein secondary structure (10-60 cm^-1 ). In this case, would gmx dos be viable given no limitations on computing resources? I understand that in order to calculate density of states, one needs a simulation with integration steps every 1-2 fs and saved trajectories about every 2-4 fs. What would be considered a long enough simulation to be meaningful? What would be required to show sufficient convergence? Is it simply a matter of replicates or something more? From my experience with liquids, 100 ps is enough for a liquid with low viscosity, but not for a liquid with high viscosity. Then there are typically hundreds of molecules to average over. What that means for a protein is hard to tell, but for sure you need 100 times the time scale (of 10 ps) to come up to the same level of sampling, then the protein is very viscous compared to a liquid, structure and dynamics have a long correlation time. If you have a truly stable protein you may be better of doing a normal mode analysis. Thank you, Daniel *Daniel Kneller* Postdoctoral Research Associate Neutron Scattering Division Neutron Sciences Directorate Oak Ridge National Laboratory -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] What is the difference between density of states (gmx dos) and vibrational power spectrum (gmx velacc -os)?
Den 2020-02-05 kl. 19:49, skrev Kneller, Daniel: Hello Gromacs Gurus, I'm studying the vibration dynamics of protein. I'm trying to calculate the density of states (dos) for protein in an MD simulation. Dos is supposed to be calculated by a Fourier transform of the velocity autocorrelation function. Both gmx dos and gmx velacc with the -os option appear in the documentation to do this but they give different plots with different axis. Both tools need long simulations where velocities are saved often, say every few fs. Then they need converged simulations, which is not going to happen with a protein. These tools are more geared for simulations of liquids. Can someone clarify the difference between these two calculations? Thank you for your time, Daniel Kneller Postdoctoral Research Associate Neutron Scattering Division Neutron Sciences Directorate Oak Ridge National Laboratory -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Regarding calculation of configurational entropy
] = -0.000126223 eigval[5314] = -0.00012707 eigval[5315] = -0.000127687 eigval[5316] = -0.000127919 eigval[5317] = -0.000128714 eigval[5318] = -0.000129043 eigval[5319] = -0.00012939 eigval[5320] = -0.000129535 eigval[5321] = -0.000130664 eigval[5322] = -0.000131691 eigval[5323] = -0.000132264 eigval[5324] = -0.000133152 eigval[5325] = -0.00013381 eigval[5326] = -0.000134219 eigval[5327] = -0.000135764 eigval[5328] = -0.000136149 eigval[5329] = -0.000138551 eigval[5330] = -0.000138698 eigval[5331] = -0.000139432 eigval[5332] = -0.000139957 eigval[5333] = -0.000140624 eigval[5334] = -0.000141187 eigval[5335] = -0.000141866 eigval[5336] = -0.000143352 eigval[5337] = -0.000143514 eigval[5338] = -0.000145445 eigval[5339] = -0.000146802 eigval[5340] = -0.00014872 eigval[5341] = -0.000149065 eigval[5342] = -0.000150165 eigval[5343] = -0.000150618 eigval[5344] = -0.000152546 eigval[5345] = -0.000154182 eigval[5346] = -0.000154271 eigval[5347] = -0.000156094 eigval[5348] = -0.00015781 eigval[5349] = -0.000158271 eigval[5350] = -0.00015992 eigval[5351] = -0.000162788 eigval[5352] = -0.000163307 eigval[5353] = -0.000166183 eigval[5354] = -0.000169429 eigval[5355] = -0.000172062 eigval[5356] = -0.000173377 eigval[5357] = -0.000173442 eigval[5358] = -0.000175975 eigval[5359] = -0.000179223 eigval[5360] = -0.000181775 eigval[5361] = -0.000183321 eigval[5362] = -0.000185641 eigval[5363] = -0.000193632 eigval[5364] = -0.000194667 eigval[5365] = -0.000232906 eigval[5366] = -0.000255899 The Entropy due to the Quasi Harmonic approximation is 27848.4 J/mol K The Entropy due to the Schlitter formula is nan J/mol K Exact command I used was: gmx anaeig -f nojumpcent1_41.xtc -v eig_heav_atom.trr -entropy -temp 298 -s prod1.tpr -n protein-H.ndx -comp eig_comp.xvg -rmsf eig_rmsf.xvg -proj eig_proj.xvg -2d 2deig_proj.xvg -b 0 -e 53 before this I had used, gmx covar -f nojumpcent1_41.xtc -s prod1.tpr -o eig_heav_atom1.xvg -v eig_heav_atom1.trr -ascii eig_heav_atom1.dat to get covariance matrix (I had also tried calculating mass weighted covariance but gmx anaeig didn't run with it). I selected Protein-H for least square fit and covariance analysis. Can you help me to understand what is going on here and if I made mistakes then what it is? Thank You Amit Kumar Did you use double precision? This is needed to get sufficient accuracy, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] How to add osmotic stress
Den 2020-02-02 kl. 17:46, skrev Alex Mathew: How to introduce osmotic stress on a simulation system to study the transportation differences in varying conditions.( protein-membrane system) Use a double membrane and different concentrations in the water phases. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Dipole moment and dielectric constant - gmx dipoles
Den 2020-01-27 kl. 01:28, skrev Iman Ahmadabadi:
Dear Philip,
Yes, you are right, thank you very much for your time and kindness.
gmx trjconv -pbc whole
Best regards,
Iman
On Sun, Jan 26, 2020 at 4:17 PM Iman Ahmadabadi
wrote:
Dear Gromacs users,
I'm trying to reproduce the gmx dipoles results via python code. In
calculating the fluctuations of total dipole moment, which is the sum on
dipole moment of individual molecules in the box, M = \sum q_{i}*R_{i}, in
which the charges q_{i} are in electron unit and position R_{i} are in nm.
For calculating M for each time step (frame), the x,y, and z component of
each atom is multiplied to their charges, and then summing on all atoms.
The average of M is on all trajectory frames, meaning that summing on M for
all frames and then dividing by the number of frames. Here, the acquired M
is divided by proper constant (0.020819434 e
<https://en.wikipedia.org/wiki/Elementary_charge>·nm
<https://en.wikipedia.org/wiki/Nanometre>) to set it in the Debye unit.
For M^{2}, M.M (dot product of M by M) is calculated for each frame and
then summing on all frames, followed by dividing by the number of frames.
But the results are larger than gmx dipoles, I wanted to ask that there is
something gmx dipoles is using in order to calculate the and ,
causing this difference? I appreciate any help in this regard.
Best regards,
Iman
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Gromacs Users mailing list
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Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize
Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino: Ok, thank you. I am counting the elements assuming they are in an array organized in a row major fashion. have you tried supplying -n1 47 -n2 35 to be able to check manually? (by the way a resolution of 0.1 Angstrom is unlikely to give you a smooth surface) Scarica Outlook per Android<https://aka.ms/ghei36> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Berk Hess Sent: Wednesday, January 22, 2020 6:34:47 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size A grid element I looked at the code and it directly uses n1 and n2 you provide. So I thought that it might be that the code reading the file has a limit on the number of characters on a line. /Berk From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Michele Pellegrino Sent: Wednesday, January 22, 2020 5:07 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size What do you mean by 'element'? Anyway, part of the issue was in how I was reading the file; with a little modification of the script I reduced the mismatch, but it still persists. Could it be because GROMACS forces a grid with same meshwith in x and (in my case) z direction, so that the used should impose either -n1 OR -n2 (but not both)? Or maybe the issue is just in the format of the .dat output file? By the way, the simulation box is 47.72970 x 5.51140 x 35.37240 nanometers (if that may help understanding the issue). Thanks, Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Berk Hess Sent: 22 January 2020 16:49 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] .dat file from gmx densmap does not match prescribed size How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit. /Berk From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Michele Pellegrino Sent: Tuesday, January 21, 2020 5:16 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] .dat file from gmx densmap does not match prescribed size Hello, I am struggling a little bit with gmx densmap. I am trying to obtain a matrix with density values from the .dat file generated by the program; however the number of data in the output file does not match what I am expecting. I tried to prescribe both the number of bins in each direction (-n1 and -n2 options) and the grid size (-bin option), not at the same, of course: gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -n1 4772 -n2 3531 OR (equivalently): gmx densmap -f traj.trr -s system.tpr -od densmap.dat -b 800.0 -e 1200.0 -aver y -bin 0.01 In both cases I get a dimension mismatch (I expect 16849932 values but I get 4359553). I am using GROMACS 2019.4?. What am I doing wrong? Thanks for your help. Cheers, Michele -- 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. -- 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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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
Re: [gmx-users] lifetime of hydrogen bond
Den 2020-01-02 kl. 07:47, skrev sp...@iacs.res.in: Dear all I want to calculate the hydrogen bond lifetime of a dynamic hydrogen bond which stays for say 10 ns (as I have saved the trajectory with 10 ps interval). I am trying to calculate the lifetime of this hydrogen bond by gmx hbond command gmx hbond -f traj_nopbc.trr -s md.tpr -n index.ndx -num hbond_G4_N3_131_N3H4.xvg -dist dist_G4_N3_131_N3H4.xvg -ang ang_G4_N3_131_N3H4.xvg -life life_G4_N3_131_N3H4.xvg Its give me a "uninterrupted hydrogen bond lifetime" plot which stays for 200 ps. I cannot understand the meaning of this plot. How to explain this 200 ps lifetime? Thanks sunipa The -life option does not give you a meaningful answer since it is sensitive to small fluctuations. My oldpaper in J. Phys. Chem. B 110 pp. 4393-4398 (2006) explains it in detail. You can rerun without -life and with the -ac flag. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Force (%)" value in md.log file
Den 2019-12-19 kl. 12:21, skrev Pragati Sharma: Hello all, I am simulating a polymer system (3 atoms, 2fs time step, PME) on a workstation with CPU: 2X6 cores (24 logical) and 2 2080 RTX GPUs. I am running the 2 separate simulations using 10 threads and 1 GPU each using command: *gmx_tmpi mdrun -v -deffnm md2 -nb gpu -gpu_id 1 -nt 10* I found that the force values (%) are very high in md.log file. *Is this unusual ? If yes, how to decrease this value?* MD is all about computing forces, the higher fraction of computer time goes to this, the less overhead. The benchmark you refer to below seems the strange one instead. *Excerpts from md.log file* "On 1 MPI rank, each using 10 OpenMP threads Computing: Num Num Call Wall time Giga-Cycles RanksThreads Count (s) total sum% - Neighbor search 1 10 1001 4.724 160.233 3.4 Launch GPU ops. 1 10 22 10.971372.134 7.9 * Force1 10 11 80.756 2739.287 57.9* Wait PME GPU gather1 10 11 0.472 16.007 0.3 Reduce GPU PME F 1 10 11 2.185 74.127 1.6 Wait GPU NB local 1 10 11 0.591 20.042 0.4 NB X/F buffer ops. 1 10 199001 12.043 408.514 8.6 Write traj. 1 10 11 0.337 11.429 0.2 Update 1 10 11 4.054 137.5202.9 Constraints 1 10 13 19.981 677.77614.3 Rest3.326 112.803 2.4 - Total139.440 4729.873 100.0 " I am comparing with a published benchmark having values for "*Force= 14.9%".* -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Young's modulus
Den 2019-12-15 kl. 09:09, skrev Iman Katouzian: Good day, How can I calculate Young and shear modulus using GROMACS package? Thanks. Gromacs is typically used for liquid state simulations although it is possible to simulate solid state as well. For the liquid state you can compute the related compressibility, see e.g. Eqn 11 in J. Chem. Theor. Comput. 8 pp. 61-74 (2012) This can likely be extended to solids as well. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] rotacf error
Den 2019-12-15 kl. 04:13, skrev Mario Andres Rodriguez Pineda: Hi all I want to calculate the order parameter of the NH vector for each amino acids of a protein in a gromacs trajectory for compare with NMR experimental data. I found that it can be calculated using rotacf to calculate the correlation time, when trying to run the program I get an error. In the attached file I show more details about the error andhow I created the index. Could you help me to correct the index for calculate the correlation time and in turn the order parameter S2? Thanks for your help. you likely have Proline residues in your protein which do not have a H. More tricky, if you have two prolines you get an even number of atoms again but it can be completely wrong. Solution is to remove prolines in make_ndx before you select a group of NH. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Generalized Born solvation
Den 2019-12-04 kl. 20:20, skrev Ling Chan: Hello colleagues, Is it that the Generalized Born solvation model has been dropped, and that there is no replacement for it? I am not after free energy numbers. I would just like to carry out MD without a periodic boundary, and account for water effects using the Born model. You can use an older version of gromacs, but it will be difficult to get any publishable results. This is why it was dropped. There are tons of articles comparing explicit and implicit solvent and they all have similar conclusions. Thank you! Ling ( You can compare the last line of http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html with http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html#mdp-value-implicit-solvent=GBSA ) Notice of Confidentiality: The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, re-transmission, dissemination or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error please contact the sender immediately by return electronic transmission and then immediately delete this transmission including all attachments without copying, distributing or disclosing the same. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Lipidbook webpage is off - is it possible to find its content somewhere?
Den 2019-12-04 kl. 01:21, skrev Oliver Beckstein: Hi Daniel, We had technical issues with the “server” that Lipidbook was running on (an old ~2006 MacMini…). We are in the process of moving it to a more reliable platform. However, that hasn’t been easy so it’s been dragging on for too long. However, I am happy to say that we are currently working on it. We will update https://twitter.com/lipidbook <https://twitter.com/lipidbook> once https://urlproxy.sunet.se/canit/urlproxy.php?_q=aHR0cHM6Ly93d3cubGlwaWRib29rLm9yZw%3D%3D&_s=c3BvZWxAeHJheS5ibWMudXUuc2U%3D&_c=43045c21&_r=dXUtc2U%3D <https://urlproxy.sunet.se/canit/urlproxy.php?_q=aHR0cHM6Ly93d3cubGlwaWRib29rLm9yZy8%3D&_s=c3BvZWxAeHJheS5ibWMudXUuc2U%3D&_c=bade93c1&_r=dXUtc2U%3D> is operational again. I should also say that lipidbook was built when it was actually not easy to find lipid parameters and it provided a repository for people to deposit their parameters so that others could easily re-use them. Nowadays this seem to be a less pressing need but there still seem to be some parameter sets stored that are difficult to find elsewhere. However, the structure of the site is not simple so I can’t just make a bunch of files available. I’m sorry, you’ll have to wait until the site is up again — apologies again. It might also be wise to reconsider these parameters that by now are likely somewhat oldish. If memory serves me well both Peter Tieleman and Jochen Hub supply some lipid / membrane parameters on their websites. Oliver On Dec 3, 2019, at 4:31 PM, daniel depope wrote: Every now and than I came across reference to, so called "lipidbook" ( https://lipidbook.bioch.ox.ac.uk/ ), which, as stated, contains force field parameters for various lipids.But webpage is obviously off for a long time, so I never have an opportunity to see its content. Moreover it looks very strange to me that literally nobody talks about that issue on the internet, although, as it seems, "everyone" used it in their work! So question is: is it possible to find its content somewhere? Thanks -- Oliver Beckstein, DPhil * oliver.beckst...@asu.edu https://becksteinlab.physics.asu.edu/ Associate Professor of Physics Arizona State University Center for Biological Physics and Department of Physics Tempe, AZ 85287-1504 USA Office: PSF 348 Phone: +1 (480) 727-9765 FAX: +1 (480) 965-4669 Department of Physics: https://physics.asu.edu/content/oliver-beckstein Center for Biological Physics: https://cbp.asu.edu/content/oliver-beckstein -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] solvent evaporation modeling
Den 2019-12-02 kl. 00:03, skrev SAKO MIRZAIE: Hi All, I want to simulate a polymer: protein system in a way that water solvent will evaporated gradually. How should I do that? What parameters are needed to be included in the mdp file. Best Alexandra Patriksson, Erik Marklund and David van der Spoel: Proteins Structures under Electrospray Conditions Biochemistry 46 pp. 933-945 (2007) Yaofeng Wang, Daniel Larsson and David van der Spoel: Encapsulation of Myoglobin in a CTAB micelle - A Simulation Study Biochemistry 48 pp. 1006-1015 (2009) Erik Marklund, Daniel Larsson, Alexandra Patriksson, David van der Spoel & Carl Caleman: Structural stability of electrosprayed proteins: temperature and hydration effects Phys. Chem. Chem. Phys. 11 pp. 8069-8078 (2009) Friemann, Rosmarie; Larsson, Daniel; Wang, Yaofeng; Van der Spoel, David: Molecular Dynamics Simulations of a Membrane Protein-Micelle Complex in vacuo J. Amer. Chem. Soc. 131 pp. 16606-16607 (2009) And a review in David van der Spoel, Erik G. Marklund, Daniel S. D. Larsson and Carl Caleman: Proteins, Lipids and Water in the Gas Phase Macromolecular Bioscience 11 pp. 50-59 (2011) -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] toluene as a slovent
Den 2019-12-02 kl. 17:10, skrev Mijiddorj B: I recommend you to use (1) gmx insert-molecules tool to fill the box that solvent molecule. For the number of molecules, you can use as much as a higher number using -nmol option. The result tells you, how many molecules inserted from ordered numbers. (2) Then, you should manually edit the topology file using the correct number of toluene. http://virtualchemistry.org/molecule.php?filename=toluene.sdf http://virtualchemistry.org/ff.php -- Message: 5 Date: Mon, 2 Dec 2019 12:14:21 +0330 From: Iman Katouzian To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] toluene as a slovent Message-ID: Content-Type: text/plain; charset="UTF-8" Hello, I have downloaded the toluene pdb file and want to use it as solvent in GROMACS rather than the water molecules. I have added toluene as a molecule using gmx solvate -cs toluene.gro however, in the next steps, it is not added to the topol.top file and I cannot go-ahead to the next steps of simulation. I'd be grateful if someone can help me with this issue as I have not tried other solvents rather than water before. Thanks. On Sun, Dec 1, 2019 at 4:04 PM Iman Katouzian wrote: Hello, I have downloaded the toluene pdb file and want to use it as solvent in GROMACS rather than the water molecules. I have added toluene as a molecule using gmx solvate -cs toluene.gro however, in the next steps, it is not added to the topol.top file and I cannot go-ahead to the next steps of simulation. I'd be grateful if someone can help me with this issue as I have not tried other solvents rather than water before. Thanks. -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- -- 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. End of gromacs.org_gmx-users Digest, Vol 188, Issue 3 ************* -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Toluene .rtp
Den 2019-11-28 kl. 12:50, skrev Iman Katouzian: Hello, I wonder if somebody can help me where I can find the parameters for *toluene *solvent so that I can add it to the .rtp file for addition to my protein system as for the solvent I want to add this type and NOT water molecules. Thanks Here is simulation data for toluene http://virtualchemistry.org/molecule.php?filename=toluene.sdf and here are input files: http://virtualchemistry.org/ff.php -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] anisotropic polarization
Den 2019-11-22 kl. 09:53, skrev Amin Rouy: Hi, Is anisotropic polarization implemented in Gromacs. I find a paper by Justin; ''Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model'' How can I apply it to my own molecules? Thank you for help. There is just one (rather obscure) anisotropically polarizable water model implemented. There is a topology called sw.itp, but there are better (isotropic) models out there. https://pubs.acs.org/doi/10.1021/jp003843l -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Vibrational frequencies from gromacs trajectory
Den 2019-11-09 kl. 08:28, skrev Bakary N'tji Diallo: Hello Can we compute bond and angle vibrational frequencies from a gromacs simulation trajectory using gromacs analysis tools or importing the trajectory in another simulation analysis package? Thanks Do you mean from MD? In that case a covariance analysis can be done. To get the pure frequencies it is better to use normal mode analysis. Please look these items up in the manual! -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Regarding force field for silicon oxide
Den 2019-11-05 kl. 01:59, skrev Mijiddorj B: Dear Prof. David van der Spoel, Thank you very much for your reply and sending an amazing work. I am sorry for asking further questions. Can you give me an advice to use the parameters which were considered in the ref#44 in this work? Ref#44 uses the OPLS force field and expresses LJ parameters for the contents. The OPLS files for gromacs 4.6 contain this non-standard addition to nonbonded types This is what was used in my paper and ref 44. Note that there is no GROMACS force field, so just refer to this as parameters used in those papers. ; Added by DvdS 05/2005 copied from GROMACS force field. SI SI 14 28.08000 0.000 A3.38550e-01 2.44704e+00 Best regards, Mijiddorj -- Message: 4 Date: Fri, 1 Nov 2019 17:44:38 +0100 From: David van der Spoel To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Regarding force field for silicon oxide Message-ID: <68c1ff39-9979-14ac-a1f9-eb1788be0...@xray.bmc.uu.se> Content-Type: text/plain; charset=windows-1252; format=flowed Den 2019-11-01 kl. 17:07, skrev Mijiddorj B: I would like to simulate a system which contains a silicon oxide surface and a polymer. Is it possible to simulate in gromacs? I thought that GROMOS force field could be applied in this purpose. Is it right? I am not sure. If you have a potential function that supports it and software to build topologies it works, e.g.: David van der Spoel, Erik J. W. Wensink and Alex C. Hoffmann: Lifting a glass from a wet table: a microscopic picture Langmuir 22 pp. 5666-5672 (2006) http://pubs.acs.org/cgi-bin/download.pl?la053284f/X8nx However please do not ask me for the files :) Also, is it possible to use InterfaceFF and Charmm force fields for this system? I mean that the silicon oxide could be treated by InterfaceFF, and CharmmFF could be applied for polymer structure. Do you have any experience, please let me advice. Thanks for your help. Best regards, Mijiddorj -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] cmake fails with custom gcc version
Den 2019-11-02 kl. 14:25, skrev Mahmood Naderan: Hi, Although I have specified a custom CC and CXX path, the cmake command fails with an error. $ cmake .. -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=../single61 -DGMX_BUILD_OWN_FFTW=ON -DGMX_CUDA_TARGET_SM=61 -DCMAKE_C_COMPILER=/home/mahmood/tools/gcc-6.1.0/bin/gcc -DCMAKE_CXX_COMPILER=/home/mahmood/tools/gcc-6.1.0/bin/g++-- The C compiler identification is unknown -- The CXX compiler identification is unknown -- Check for working C compiler: /home/mahmood/tools/gcc-6.1.0/bin/gcc-- Check for working C compiler: /home/mahmood/tools/gcc-6.1.0/bin/gcc -- brokenCMake Error at /home/mahmood/tools/cmake-3.15.4/share/cmake-3.15/Modules/CMakeTestCCompiler.cmake:60 (message): The C compiler "/home/mahmood/tools/gcc-6.1.0/bin/gcc" is not able to compile a simple test program. Have you verified that the compiler is installed correctly, e.g. by compiling a small test program? Is /home/mahmood/tools/gcc-6.1.0/bin/ in your PATH? It fails with the following output: Change Dir: /home/mahmood/cactus/gromacs/gromacs-2019.4/build/CMakeFiles/CMakeTmp Run Build Command(s):/usr/bin/gmake cmTC_68dcc/fast && /usr/bin/gmake -f CMakeFiles/cmTC_68dcc.dir/build.make CMakeFiles/cmTC_68dcc.dir/build gmake[1]: Entering directory `/home/mahmood/cactus/gromacs/gromacs-2019.4/build/CMakeFiles/CMakeTmp' Building C object CMakeFiles/cmTC_68dcc.dir/testCCompiler.c.o /home/mahmood/tools/gcc-6.1.0/bin/gcc -o CMakeFiles/cmTC_68dcc.dir/testCCompiler.c.o -c /home/mahmood/cactus/gromacs/gromacs-2019.4/build/CMakeFiles/CMakeTmp/testCCompiler.c /home/mahmood/tools/gcc-6.1.0/libexec/gcc/x86_64-pc-linux-gnu/6.1.0/cc1: error while loading shared libraries: libmpc.so.3: cannot open shared object file: No such file or directory gmake[1]: *** [CMakeFiles/cmTC_68dcc.dir/testCCompiler.c.o] Error 1 gmake[1]: Leaving directory `/home/mahmood/cactus/gromacs/gromacs-2019.4/build/CMakeFiles/CMakeTmp' gmake: *** [cmTC_68dcc/fast] Error 2 CMake will not be able to correctly generate this project. Call Stack (most recent call first): CMakeLists.txt:41 (project) -- Configuring incomplete, errors occurred! See also "/home/mahmood/cactus/gromacs/gromacs-2019.4/build/CMakeFiles/CMakeOutput.log".See also "/home/mahmood/cactus/gromacs/gromacs-2019.4/build/CMakeFiles/CMakeError.log". However, the path is correct $ /home/mahmood/tools/gcc-6.1.0/bin/gcc -vUsing built-in specs. COLLECT_GCC=/home/mahmood/tools/gcc-6.1.0/bin/gccCOLLECT_LTO_WRAPPER=/home/mahmood/tools/gcc-6.1.0/libexec/gcc/x86_64-pc-linux-gnu/6.1.0/lto-wrapperTarget: x86_64-pc-linux-gnu Configured with: ./configure --prefix=/home/mahmood/tools/gcc-6.1.0 --disable-multilib --enable-languages=c,c++Thread model: posix gcc version 6.1.0 (GCC) Any idea about that? Regards, Mahmood -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Regarding force field for silicon oxide
Den 2019-11-01 kl. 17:07, skrev Mijiddorj B: I would like to simulate a system which contains a silicon oxide surface and a polymer. Is it possible to simulate in gromacs? I thought that GROMOS force field could be applied in this purpose. Is it right? I am not sure. If you have a potential function that supports it and software to build topologies it works, e.g.: David van der Spoel, Erik J. W. Wensink and Alex C. Hoffmann: Lifting a glass from a wet table: a microscopic picture Langmuir 22 pp. 5666-5672 (2006) http://pubs.acs.org/cgi-bin/download.pl?la053284f/X8nx However please do not ask me for the files :) Also, is it possible to use InterfaceFF and Charmm force fields for this system? I mean that the silicon oxide could be treated by InterfaceFF, and CharmmFF could be applied for polymer structure. Do you have any experience, please let me advice. Thanks for your help. Best regards, Mijiddorj -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Define intermolecular interactions in L-J simulation
Den 2019-10-23 kl. 18:22, skrev Li, Shi: Dear GMX users, I am wondering if there is a way to define the intermolecular interaction to simulation a binary LJ system. For example, I have two atoms A and B, they share the same LJ parameter, and I want to change the interaction parameter between A and B, so that I would expect different behaviors from the simulation (mix or phase separation). I checked the manual and found this can be defined in the topology file as [intermolecular_interactions] and use the [pairs] interaction then list the atom pairs. But it is still confusing if I have a system containing 500 A and 500 B, how can I apply this to the entire binary system. I was assumed that I can use atomtype instead of atom number? But how and where to specify that? Any suggestions? Thanks, Shi Use [ nonbonded_types ] A A 1 c6 c12 B B 1 c6 c12 A B 1 c6 c12 -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Frozen group moves!
Den 2019-10-21 kl. 21:24, skrev Alex: Dear all, I freeze a group in my system in all directions as normal: freezegrps = GR freezedim= Y Y Y So, I was expecting that the coordinates and velocities do not get updated during the simulation, however, here is just part of in.gro and out.gro in which the coordinates and velocity components have changed. #Y #Z #Vx #Vy #Vz #Y #Z #Vx #Vy #Vz 0.271 0.049 0. 0. 0.| 0.271 0.050 0. 0. -0.0637 0.249 0.020 0. 0. 0.| 0.249 0.020 0. 0. 0.1823 0.251 0.490 0. 0. 0.| 0.251 0.490 0. 0. -0.6805 0.228 0.524 0. 0. 0.| 0.228 0.524 0. 0. -0.1568 0.251 0.055 0. 0. 0.| 0.251 0.055 0. 0. -0.4114 0.369 17.054 0. 0. 0.| 0.369 17.055 0. 0. -0.5276 0.390 0.272 0. 0. 0.| 0.390 0.273 0. 0. -0.2386 0.184 0.444 0. 0. 0.| 0.184 0.444 0. 0. -0.1694 0.365 0.444 0. 0. 0.| 0.365 0.444 0. 0. 0.1299 0.361 0.553 0. 0. 0.| 0.361 0.554 0. 0. -0.5277 Anybody knows what might be the reason and how one can avoid that to happen? Regards, Alex Do you have pressure coupling turned on? Alternatively, are the frozen coordinates part of a compound that is constrained? Both of these could cause this. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Normal Mode Analysis
Den 2019-10-16 kl. 23:31, skrev Adip Jhaveri: Hello All, I am simulating two proteins in solution and would like to perform Normal Mode Analysis on trajectory snapshots. I take one particular frame in the trajectory and minimize it, followed by mdrun for normal mode analysis. However I am getting constraint errors in each of the two steps - 1) In minimization it is recommended to use 'cg' method but this does not work and it throws an error due to the constraints present in the system. 2) I tried using the 'steep' method for minimization but then, during the normal mode mdrun, it is giving an error on constraints. How do I solve this problem? Do I completely remove the constraints and then perform 'cg' minimization and 'nm' mdrun? Yes. Regards, Adip -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] issues running virus capsid simulation
Den 2019-09-25 kl. 02:37, skrev Justin Lemkul: On 9/24/19 5:09 PM, Asis Jana wrote: Hi, I am doing viral capsid simulation using GROMACS 2018. The capsid was first energy minimized using the steepest-descent algorithm followed by 40 ns of NVT (300 K) followed by 10 ns of NPT (300 K, 1 atm) equilibration. In the NVT and NPT equilibration, the heavy atoms of the protein were restrained with a force constant of 1000 kJ/mol/nm. Production MD simulations were performed for 400 ns at a temperature of 300 K and a pressure of 1 atm. Please see the production mdp file below. title = MD simulation ; Run parameters integrator = md nsteps = 20 dt = 0.002 ; Output control nstxout = 5 nstvout = 5 nstenergy = 5 nstlog = 5 nstxout-compressed = 5 compressed-x-grps = System continuation = yes constraint_algorithm = lincs constraints = h-bonds lincs_iter = 1 lincs_order = 4 ; Neighborsearching cutoff-scheme = Verlet ns_type = grid nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw_switch = 1.0 rvdw = 1.2 pme_order = 4 fourierspacing = 0.16 ; Temperature coupling is on tcoupl = Nose-Hoover tc-grps = Protein Non-Protein tau_t = 1.0 1.0 ref_t = 300 300 ; Pressure coupling is on pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 5.0 ref_p = 1.0 compressibility = 4.5e-5 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off nstcomm = 100 comm_mode = linear comm_grps = Protein Non-Protein I have attached RMSD and Rg plots with this mail. It looks like that capsid is stiil not equilibrated. Rg is increasing rapidly, whereas RMSD of the capsid is increasing slowly. Please see the attached plots. Any kind of advice or suggestions are deeply appreciated. The mailing list does not accept attachments. To share images, upload them to a file-sharing service and provide a URL. What do your eyes tell you when you visualize the trajectory? Do the data make sense? Have you accounted for periodicity effects? Are there simply structural changes happening? Nothing says any structural metric has to level off in some convenient amount of time. Indeed, big things take long time to equilibrate. For a virus it may depend on whether a genome is present, ions etc. We did this stuff8 years ago and it take many microseconds: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002502 https://pubs.acs.org/doi/abs/10.1021/ct3002128 -Justin -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Regarding obtaining potential energy using energy groups
Den 2019-09-14 kl. 23:32, skrev Najamuddin Memon: It depends on interaction of proteins i.e A interacts with B A&B both interact with C Only A or only B interacts with C In 2nd option you can make one group (A&B) and 2nd group as C Note that this only tells you about non-bonded interaction at short range. In order to also include the long range (PME), checkout this paper: J. Chem. Theor. Comput. 9 pp. 4542-4551 (2013) (supporting info in particular). Then you still do not have grouped energies for the bonded forces since this is not implemented and finally you have to ask yourself what does an interaction energy mean? On Sun, Sep 15, 2019, 12:28 AM Nashit Jalal 17250017 < nashit.ja...@iitgn.ac.in> wrote: I think so that the question is to confirm whether finding potential energy making (AB) and C as 2 groups similar to the potential energy obtained by adding energies obtained by making A -C and B -C as groups -Nashit On Sun, Sep 15, 2019 at 12:10 AM Najamuddin Memon < najamuddinmemo...@gmail.com> wrote: No you should take two groups at a time Like A VS B then A vs C and so on before doing energy analysis you should make index file that you have to call in command line with -n index.ndx Regards Najam On Fri, Sep 13, 2019, 3:21 PM Nirali Desai < nirali.d.ims...@ahduni.edu.in> wrote: Dear all I have a system with 3 protein chains A B and C. I want to calculate the potential energy between different chains. I created energy groups by creating a new index file. If I calculate potential energy between C as one group and (AB) as another group, will it contain the potential energy of interaction between A and B too? Your kind guidance in this matter is highly appreciated. Thanking you, Nirali Desai -- 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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Batch mode error in GROMACS version 2019.2
Den 2019-09-14 kl. 08:36, skrev Rajib Biswas: I did some more experimentation about this and found that this error is coming only with the mpi enabled version. please give the exact command line Rajib On Fri, Sep 13, 2019 at 10:58 PM Rajib Biswas wrote: Hi Mark, Thanks! Interactively I could do it without any error. However, this error only arises whenever I have tried to use batch mode. With regards, *Rajib* On Fri, Sep 13, 2019 at 6:06 PM Mark Abraham wrote: What happens when you do it interactively? Mark On Fri, 13 Sep 2019 at 14:21, Rajib Biswas wrote: Dear All, I am trying to use the post-processing tools in batch mode. I am using the following commands echo 18 0 | gmx_mpi energy -f traj.edr -o temperature Getting the following error: Program: gmx energy, version 2019.2 Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296) Fatal error: No energy terms selected I have even tried all the options mentioned http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts however, could not get it worked for version 2019.2. Any help will be appreciated. With regards, *Rajib* -- 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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] How to use gmx h2order when using four point water model
Den 2019-09-11 kl. 04:38, skrev Jun Zhou: Hi all, I want to obtain the water dipole orientation at the interface using gmx h2order. It works well when I I use 3 point water model, like SPC/E. The manual says that the order of water should be O H H, but for 4 point water model, there is a vitual atom, and this command cannot output the correct results. Is there any solutions for this poblem? Thanks, Jun You can use trjconv to remove the virtual site from the trajectory, maybe it even works in the tool directly, without running trjconv. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] pressure is coming 1.39
Den 2019-09-08 kl. 06:36, skrev Bratin Kumar Das: Thanks sir for your reply. My target pressure was 1 atm.. The fluctuations depend on the system size as 1/sqrt(natoms). To obtain a std dev of 3 bar you need a really big system. On Sat 7 Sep, 2019, 8:15 PM Mark Abraham, wrote: Hi, Without a statistical error estimation and a target pressure, the question can't be answered. Pressure takes time to measure, and you need to do so only after equilibration. 1.39 +/- 3 bar might be fine Mark On Sat., 7 Sep. 2019, 07:48 Bratin Kumar Das, <177cy500.bra...@nitk.edu.in wrote: Hi,, I am doing a simulation of peptide in water. After 10 ns npt equilibration the average pressure is coming 1.39 and density is coming 1005.71 kg/m3. Can I proceed for production run? And what is the upper and lower limit for the pressure ...after which we can continue production run? -- 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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] How to Calculate tetrahedral order parameter
Den 2019-09-03 kl. 14:02, skrev Soham Sarkar: Sorry, I forgot to mention that I have two systems. One consists of protein-water and the other one consists of protein-water-urea. I need to calculate the tetrahedral order parameter of water around the protein within 0.4nm for these two systems. Sounds like a very difficult problem. I assume you want to evaluate whether the structure is more ordered close to the protein than in bulk. In theory you could find all the water molecules with a radius X from the protein, using gmx trjorder and then generate an index that you pass to gmx hydorder. However if you use a shell of 0.4 nm there will not be enough water to test this, and in addition the water interacting with the protein will not be counted by the program. The most important question you should ask your self is whether you want to get out something that can be measured, in that case you would be better off computing free energies. Thanks and regards- Soham On Tue, 3 Sep 2019, 5:24 pm David van der Spoel, wrote: Den 2019-09-03 kl. 13:26, skrev Soham Sarkar: Dear all, I know this question was asked by many users before but searching them all I did not get how to perform it in GROMACS. Please help me with this. Is there any in built command line exist for Tetrahedral order parameter calculation? If gmx hydorder is the existing tool for calculating tetrahedral order parameter, went through this I did not understand the usage of it too. Thanks in advance- Soham What system, water? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] How to Calculate tetrahedral order parameter
Den 2019-09-03 kl. 13:26, skrev Soham Sarkar: Dear all, I know this question was asked by many users before but searching them all I did not get how to perform it in GROMACS. Please help me with this. Is there any in built command line exist for Tetrahedral order parameter calculation? If gmx hydorder is the existing tool for calculating tetrahedral order parameter, went through this I did not understand the usage of it too. Thanks in advance- Soham What system, water? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Question about Gromacs
Den 2019-08-26 kl. 20:53, skrev Najla Hosseini: Dear David, Hope you are doing well. I am Gromacs user and I need to change the partial charge of molecules in force field or itp file as a function of distance during the run in Gromacs. Is it possible? How I should do that? Please pose your questions on the mailing list, however this is not possible to dynamically. If not, I should use two itp file with a condition for finishing one of them and starting the new tpr file based on another itp file, how I should do that? Thank you so much. I really appreciate your consideration and time. Best Regards, Najla -- /*Kind Regards, */ /*Najla * / -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Not all snapshots are written to trr during minimization
Den 2019-08-18 kl. 17:10, skrev Dawid das: Dear All, I noticed that after my minimization run I have less snapshots in trr than I expected. For instance, the structure is written every 126-127 steps (plus the last one) even though my mdp file states nstxout = 100 Best wishes, Dawid Grabarek Only writes when the energy goes down. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Regarding too many LINCS warnings for bicarbonate ion
4 5 3 27.19600 -7.94960 -19.24640 0.00.00.0 ; O2-C1-O3-H1 [ dihedrals ] ; impropers ; treated as propers in GROMACS to use correct AMBER analytical function ;i j k l func phase kd pn 1 3 2 4 1 180.00 4.60240 2 ; O1-O2- C1-O3 -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] PRESS-XX, PRESS-YY, PRESS-ZZ in .edr file
Den 2019-08-05 kl. 05:48, skrev Anh Vo: Hi all, I have searched online and GROMACS documentation for this question but I haven't found any clear definition yet. Please help me to clarify it. In the output .edr file, there are PRESS-XX, PRESS-YY and PRESS-ZZ options. What do they represent? Are they principal pressures (stresses) averaged for all atoms during the simulation? What is the difference between those options and PRESSURE option? Thank you very much. Best, Anh Vo THe pressure is a tensor, see manual. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Regarding OH, HH vector distribution
Den 2019-07-31 kl. 15:00, skrev Omkar Singh: I calculated these two vectors with Z-axis now I want to make distribution plot p(costheeta) Vs cos(theeta). How can I plot because it is giving the value only theeta. Is there any command. Try write your own script. Thanks On Wed, Jul 31, 2019, 12:00 David van der Spoel wrote: Den 2019-07-31 kl. 06:12, skrev Omkar Singh: Thanks Sir, I did like that only, Now how can I make the distribution plot for these vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command. But results is not proper. Can you suggest me regarding this? Thank you How about gmx gangle -oh ? On Tue, Jul 30, 2019, 17:27 David van der Spoel wrote: Den 2019-07-30 kl. 07:55, skrev Omkar Singh: Hi, I did by "gmx gangle ..." command. But I am not getting good result, because I have a doubt in ndx file. Can you help me for making ndx file. How should I select the atom for vectors. For OH it should be 1 2 1 3 4 5 4 6 7 8 7 9 etc., assuming a three particle water model with atoms O H H. For HH it should be 2 3 5 6 8 9 etc. A simple script would do it. The dipole vector is somewhat harder. Thanks On Mon, Jul 29, 2019, 22:50 David van der Spoel wrote: Den 2019-07-29 kl. 18:26, skrev Omkar Singh: Hi, Meaning is that If I want to calculate angle between OH, HH and dip vector with positive Z-axis. How can I make index file for this issue? And is it possible that the angle distribution of these vectors for bulk water aproximatly linear. Hope now question is clear. Probably. Check gmx gangle -g2 z Thanks On Mon, Jul 29, 2019, 16:33 David van der Spoel < sp...@xray.bmc.uu.se> wrote: Den 2019-07-29 kl. 12:24, skrev Omkar Singh: Hello everyone, Is it possible that the probability distribution of HH, OH vector for bulk water is approximately linear? What do you mean? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] GROMOS 54a7 mapping warning
Den 2019-07-31 kl. 15:21, skrev Gselman, Larissa: Hallo everyone, I want to simulate a peptide with the Gromos 54a7 force field. Your structure is missing atoms, please fix and rerun without -ignh. So, my first command is: gmx_mpi pdb2gmx -f Mh.pdb -o Mh_processed.gro -water spce -ignh -inter I choose 14 for the Gromos 54a7 ff, then I choose the protonation state the titratable amino acids and for the termini I choose the zwitterionic state (so I choose 0 and 0). But this results in the following warnings: WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 38 named ASN of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. This is the beginning and end of my pdb file with ASP as first and ASN as last amino acid: ATOM 1 N ASP A 1 59.994 60.432 82.286 1.00 7.49 ATOM 2 CA ASP A 1 59.341 61.407 81.415 1.00 7.49 ATOM 3 HA ASP A 1 58.651 60.833 80.799 1.00 7.49 ATOM 4 CB ASP A 1 58.494 62.384 82.263 1.00 7.49 ATOM 5 HB1 ASP A 1 59.114 63.222 82.584 1.00 7.49 ATOM 6 HB2 ASP A 1 58.142 61.868 83.157 1.00 7.49 ATOM 7 CG ASP A 1 57.247 62.920 81.535 1.00 7.49 ATOM 8 OD1 ASP A 1 57.107 62.729 80.305 1.00 7.49 ATOM 9 OD2 ASP A 1 56.369 63.525 82.180 1.00 7.49 ATOM 10 C ASP A 1 60.313 62.117 80.435 1.00 7.49 ATOM 11 O ASP A 1 61.524 61.881 80.391 1.00 7.49 . . . ATOM623 N ASN A 38 49.792 47.722 37.078 1.00 13.81 ATOM624 H ASN A 38 50.649 48.244 36.922 1.00 13.81 ATOM625 CA ASN A 38 48.636 48.172 36.306 1.00 13.81 ATOM626 HA ASN A 38 48.705 49.256 36.233 1.00 13.81 ATOM627 CB ASN A 38 48.757 47.594 34.881 1.00 13.81 ATOM628 HB1 ASN A 38 49.688 47.938 34.433 1.00 13.81 ATOM629 HB2 ASN A 38 47.934 47.954 34.264 1.00 13.81 ATOM630 CG ASN A 38 48.756 46.074 34.842 1.00 13.81 ATOM631 OD1 ASN A 38 49.775 45.434 34.642 1.00 13.81 ATOM632 ND2 ASN A 38 47.621 45.445 35.027 1.00 13.81 ATOM633 1HD2 ASN A 38 46.815 45.983 35.313 1.00 13.81 ATOM634 2HD2 ASN A 38 47.668 44.445 35.083 1.00 13.81 ATOM635 C ASN A 38 47.283 47.875 36.982 1.00 13.81 ATOM636 O ASN A 38 47.185 47.311 38.072 1.00 13.81 TER I hope you can help me and maybe tell me why this problem occurs and what I have to change. Thank you very much! Best regards Larissa -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Regarding OH, HH vector distribution
Den 2019-07-31 kl. 06:12, skrev Omkar Singh: Thanks Sir, I did like that only, Now how can I make the distribution plot for these vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command. But results is not proper. Can you suggest me regarding this? Thank you How about gmx gangle -oh ? On Tue, Jul 30, 2019, 17:27 David van der Spoel wrote: Den 2019-07-30 kl. 07:55, skrev Omkar Singh: Hi, I did by "gmx gangle ..." command. But I am not getting good result, because I have a doubt in ndx file. Can you help me for making ndx file. How should I select the atom for vectors. For OH it should be 1 2 1 3 4 5 4 6 7 8 7 9 etc., assuming a three particle water model with atoms O H H. For HH it should be 2 3 5 6 8 9 etc. A simple script would do it. The dipole vector is somewhat harder. Thanks On Mon, Jul 29, 2019, 22:50 David van der Spoel wrote: Den 2019-07-29 kl. 18:26, skrev Omkar Singh: Hi, Meaning is that If I want to calculate angle between OH, HH and dip vector with positive Z-axis. How can I make index file for this issue? And is it possible that the angle distribution of these vectors for bulk water aproximatly linear. Hope now question is clear. Probably. Check gmx gangle -g2 z Thanks On Mon, Jul 29, 2019, 16:33 David van der Spoel wrote: Den 2019-07-29 kl. 12:24, skrev Omkar Singh: Hello everyone, Is it possible that the probability distribution of HH, OH vector for bulk water is approximately linear? What do you mean? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Regarding OH, HH vector distribution
Den 2019-07-30 kl. 07:55, skrev Omkar Singh: Hi, I did by "gmx gangle ..." command. But I am not getting good result, because I have a doubt in ndx file. Can you help me for making ndx file. How should I select the atom for vectors. For OH it should be 1 2 1 3 4 5 4 6 7 8 7 9 etc., assuming a three particle water model with atoms O H H. For HH it should be 2 3 5 6 8 9 etc. A simple script would do it. The dipole vector is somewhat harder. Thanks On Mon, Jul 29, 2019, 22:50 David van der Spoel wrote: Den 2019-07-29 kl. 18:26, skrev Omkar Singh: Hi, Meaning is that If I want to calculate angle between OH, HH and dip vector with positive Z-axis. How can I make index file for this issue? And is it possible that the angle distribution of these vectors for bulk water aproximatly linear. Hope now question is clear. Probably. Check gmx gangle -g2 z Thanks On Mon, Jul 29, 2019, 16:33 David van der Spoel wrote: Den 2019-07-29 kl. 12:24, skrev Omkar Singh: Hello everyone, Is it possible that the probability distribution of HH, OH vector for bulk water is approximately linear? What do you mean? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Regarding OH, HH vector distribution
Den 2019-07-29 kl. 18:26, skrev Omkar Singh: Hi, Meaning is that If I want to calculate angle between OH, HH and dip vector with positive Z-axis. How can I make index file for this issue? And is it possible that the angle distribution of these vectors for bulk water aproximatly linear. Hope now question is clear. Probably. Check gmx gangle -g2 z Thanks On Mon, Jul 29, 2019, 16:33 David van der Spoel wrote: Den 2019-07-29 kl. 12:24, skrev Omkar Singh: Hello everyone, Is it possible that the probability distribution of HH, OH vector for bulk water is approximately linear? What do you mean? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Regarding OH, HH vector distribution
Den 2019-07-29 kl. 12:24, skrev Omkar Singh: Hello everyone, Is it possible that the probability distribution of HH, OH vector for bulk water is approximately linear? What do you mean? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] space dependent electric field
Den 2019-07-29 kl. 04:24, skrev Maryam: Dear all, I want to apply a space but not time dependent electric field to my system. I reviewed the source code of the electric field but it only has constant and time dependent EF (pulsed EF). Can anyone help me find out how I can change the source code to have space dependent EF without changing the defined parameters in gromacs so that I wont face the problem of changing all related subroutines? Which routines should I apply required changes if I want to add some new parameters for the space dependent EF? Thank you I assume you are looking at routine calculateForces in gromacs/src/gromacs/applied_forces/electricfield.cpp ? Please start by checking out the development version of gromacs if not. There you can extract the coordinates of the particle from the ForceProviderInput structure (see gromacs/src/gromacs/mdtypes/iforceprovider.h). To make things work quickly you can just hardcode the extra parameters you might need or abuse the existing one. Cheers, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Normal mode segmentation fault - memory problem ?
Den 2019-07-24 kl. 15:10, skrev Marlon Sidore: I would like a second opinion on the cause of this segfault. I have a protein in a vacuum. All atom. After extensive minimization, I produced a matrix .mtx. Then, on the cluster, a simple gmx_mpi nmeig -f normal.mtx -s normal.tpr leads to: Reading double precision matrix generated by GROMACS 2018.6 Sparse matrix storage format, nrow=27579, ncols=27579 [n2534:10432:0] Caught signal 11 (Segmentation fault) backtrace 2 0x0006ba2c mxm_handle_error() /var/tmp/OFED_topdir/BUILD/mxm-3.7.3111/src/mxm/util/debug/debug.c:641 3 0x0006bf7c mxm_error_signal_handler() /var/tmp/OFED_topdir/BUILD/mxm-3.7.3111/src/mxm/util/debug/debug.c:616 4 0x00036280 killpg() ??:0 5 0x00642091 _ZN17_INTERNAL3a3192c818nma_sparse_hessianEP16gmx_sparsematrixiPK10t_topologyRKSt6vectorImSaImEEiPfSA_() /scratch/DEFAUT/akira/ akira/installs/occigen/applications/gromacs/2018.6/intel/18.1/openmpi/intel/2.0.4/gromacs-2018.6/src/gromacs/gmxana/gmx_nmeig.cpp:220 6 0x00642091 gmx_nmeig() /scratch/DEFAUT/akira/akira/installs/occigen/applications/gromacs/2018.6/intel/18.1/openmpi/intel/2.0.4/gromacs-201 8.6/src/gromacs/gmxana/gmx_nmeig.cpp:471 7 0x00431cb9 _ZN3gmx12_GLOBAL__N_122CMainCommandLineModule3runEiPPc() /scratch/DEFAUT/akira/akira/installs/occigen/applications/gromacs/2018 .6/intel/18.1/openmpi/intel/2.0.4/gromacs-2018.6/src/gromacs/commandline/cmdlinemodulemanager.cpp:133 8 0x00431cb9 _ZN3gmx24CommandLineModuleManager3runEiPPc() /scratch/DEFAUT/akira/akira/installs/occigen/applications/gromacs/2018.6/intel/18. 1/openmpi/intel/2.0.4/gromacs-2018.6/src/gromacs/commandline/cmdlinemodulemanager.cpp:589 9 0x0040f788 main() /scratch/DEFAUT/akira/akira/installs/occigen/applications/gromacs/2018.6/intel/18.1/openmpi/intel/2.0.4/gromacs-2018.6/s rc/programs/gmx.cpp:60 10 0x000223d5 __libc_start_main() ??:0 11 0x0040f5e9 _start() ??:0 === Either I did something wrong while producing the matrix or I'm doing something wrong on the nmeig. S Should I have done something to restrict the analysis on the backbone (somehow) if it's a memory problem ? I'm still allocacating 100G to this analysis, I naively thought it was enough. 27500^2 * 8 equals 6 Gb. Should not be a memory problem. Have you tried using -end 82737 In that case the full matrix will be used. It may be slow though. Best, Marlon Sidore PhD - Post-doctoral fellow Institut d’Électronique et des Systèmes -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Specific heat calculations using gmx energy
Den 2019-07-15 kl. 09:24, skrev Pragati Sharma: Dear all, I am simulating a melt of polybutadiene consisting of 60 chains using OPLS forcefield. After 50 ns of NPT production run, specific heat is calculated using the command: *gmx energy -f ener.edr -fluct_props -nmol 60 -driftcorr * and the value obtained is: Enthalpy =2010.04 kJ/mol Heat capacity at constant pressure *Cp=22807.5 J/mol K* However when I calculate Cp from last 5 ns of trajectory the value is: Enthalpy =2004.05 kJ/mol Heat capacity at constant pressure *Cp=7934.66 J/mol K* Do the Cp calculation is highly dependent on the equilibration of system or I am missing something because the experimental valu is ~ 100 *J/mol K, *so the values from simulation are also high compared to experiments. *Thanks* Did you check whether the enthalpy makes a sudden drop in the beginning of the simulation? If so this will influence the fluctuations a lot. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] heat capacity collection
Den 2019-07-16 kl. 13:30, skrev Amin Rouy: Hi everyone, I try to collect the heat capacities from my set of simulations. I see that the heat capacity through gmx energy -fluct_props does not provide an output file with the heat capacities. Any suggestion how can I collect them (or how to do with an script)? thanks What kind of systems are these? I have quite a few reference data for liquids on http://virtualchemistry.org These were done using the gmx dos program that computes quantum corrections but this is not entirely trivial. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Hydrogen bond autocorrelation
Den 2019-06-18 kl. 15:58, skrev Gmx QA: Dear list, This has been discussed many times previously on the list, but I still have some questions about hydrogen bond autocorrelation functions. I have run a simulation with single molecule of a compound in water which can form exactly one inter-molecular hydrogen bond. From the hbnum.xvg time-series (i.e. the existence function) of this h-bond I then have a python-script to calculate the acf. The script seems to work because the resulting acf-function looks exactly the same as the corresponding function computed with xmgrace. But it is very different from what I get from gmx hbond -ac. I read a lot about continuous vs intermittent acfs for h-bonds, the latter being called non-continuous in the van der Spoel et al. 2006-paper I think. Is the reason for the discrepancy simply that gmx hbond -ac calculates a _different_ acf than you get from the hbnum.xvg file (and xmgrace)? Then, going forward, after I compute the acf and in the most basic case fit to y = a* exp(-t/b), does the value of b correspond to the life-time of the h-bond? Or it is the integral (from 0 to inf) that gives you the lifetime? This seems to be treated differently by different people. Thanks a bunch /PK There are a couple of details indeed, in particular for water. Water may bind with oxygen or hydrogens. When your compound provides a hydrogen bond acceptor, gmx hbond will compute the hydrogen bond between your compound and both H on a water molecule as the same H bond, unless you tell it not to with an option -nomerge. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Spectrum from nmeig command
Den 2019-06-15 kl. 16:12, skrev up201406812: Dear Gromacs users, In the spectrum output from the nmeig command, what is the meaning of intensity and what are its units? I'm using the 2018.6 version. Best regards, Leonardo Intensity has no meaning as of now, just the frequencies. I will have a summer worker implement proper calculation of intensities from next week. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] High pressure variation during NPT equilibration of Protein-ligand system.
Den 2019-05-21 kl. 07:36, skrev Seketoulie Keretsu: Dear Experts, I am performing a protein-ligand stimulation in gromacs 2018. The pressure value showed wild variation between -800 to 500 bar and showed an average pressure value of -139 bar. The reference is 1 bar. I have used the "lysozyme in water" simulation tutorial by Justin A. Lemkul as a reference. The tutorial mentioned that 7.5 (+- 160) bar was reasonable for the system. I'm not sure if the value I am getting in my simulation results (-139 bar variation in pressure) are reasonable. Kindly advise. How do i justify this ? References and suggestions will be appreciated. Thank you. This is normal. It will average out in a longer simulation. Larger boxes have less fluctuations in general. Regards, Seketoulie Note: The pressure values from the NPT are given below: # This file was created Tue May 14 21:24:43 2019 # Created by: # :-) GROMACS - gmx energy, 2018.4 (-: # # Executable: /usr/local/gromacs/bin/gmx # Data prefix: /usr/local/gromacs # Working dir: /home/biopo5/tutorial/Project4/JAK1/cmp49_jak1 # Command line: # gmx energy -f nvt.edr -o pressure.xvg # gmx energy is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @title "GROMACS Energies" @xaxis label "Time (ps)" @yaxis label "(bar)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Pressure" 0.00 -3931.674805 1.00 528.706482 2.00 27.634497 3.00 -130.418900 4.00 -491.462982 5.003.087336 6.00 -246.631638 7.00 -86.932167 8.00 -453.551422 9.00 -46.325455 10.00 270.657562 11.00 -432.105682 12.00 -578.059326 13.00 -397.159760 14.00 180.598190 15.00 -159.344788 16.00 -122.911415 17.00 470.059418 18.00 -375.501251 19.00 -310.881561 20.00 68.639618 21.00 157.454422 22.00 -619.447388 23.00 -130.864059 24.00 58.016773 25.00 -132.054276 26.00 114.288574 27.00 -108.022186 28.00 -235.894424 29.00 -398.703217 30.00 252.965332 31.00 -269.996368 32.00 -58.096252 33.00 -291.578918 34.00 15.896652 35.00 53.429890 36.00 43.522858 37.00 -442.695190 38.00 111.608665 39.00 -12.626378 40.00 -136.936111 41.00 182.577164 42.00 -68.747620 43.00 121.546547 44.00 127.403526 45.00 -248.055176 46.00 184.869797 47.00 162.962906 48.00 -387.420013 49.00 228.167648 50.00 348.351471 51.00 -462.909180 52.00 -234.574936 53.00 -224.565689 54.00 311.879456 55.00 -404.242920 56.00 -740.461182 57.00 38.036850 58.00 -677.158447 59.00 -117.842407 60.00 -20.302151 61.00 -558.201233 62.00 218.174881 63.00 -269.575531 64.00 -153.398697 65.00 178.027954 66.00 -193.050797 67.00 -590.598694 68.00 -487.503754 69.00 171.980606 70.00 84.821785 71.00 -219.844803 72.00 -228.680954 73.00 -145.632614 74.00 47.675121 75.00 -310.033478 76.00 -705.341248 77.00 212.275406 78.00 24.035654 79.00 -221.810410 80.00 -189.725708 81.00 217.696289 82.00 427.632660 83.00 249.210770 84.00 -405.385956 85.00 78.898247 86.00 -19.268747 87.00 85.342247 88.00 155.808731 89.002.646250 90.00 -284.466888 91.00 152.030930 92.00 280.804352 93.00 -182.475830 94.00 -268.784149 95.00 -470.018829 96.00 -163.642685 97.00 291.026855 98.00 -982.940430 99.000000 155.447800 100.00 77.415077 -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] gmx_clustsize
Den 2019-05-20 kl. 11:24, skrev Bratin Kumar Das: Hi, I wan to calculate the size of oligomers formed during the course of simulation. Therefore I used gmx clustsize. The command I used is given below > gmx clustsize -f md-cntr.xtc -s extend9.tpr -n protein_index.ndx -nc no_of_clust.xvg -ac avg_cluster_size -hc hist_clust.xvg -dt 100 -cut 0.6 -pbc -mol -b 0 -e 5 The calculation is ended up with an error which is given below I think it means you have one cluster during the whole simulation. Note that periodic boundary conditions are taken into account. Try reducing the cut-off distance. Back Off! I just backed up no_of_clust.xvg to ./#no_of_clust.xvg.2# Back Off! I just backed up avg_cluster_size.xvg to ./#avg_cluster_size.xvg.2# Back Off! I just backed up maxclust.xvg to ./#maxclust.xvg.3# Back Off! I just backed up temp.xvg to ./#temp.xvg.3# Reading frame 0 time0.000 Reading file extend9.tpr, VERSION 2016.5 (single precision) Reading file extend9.tpr, VERSION 2016.5 (single precision) Using molecules rather than atoms. Not reading index file protein_index.ndx Last frame 5000 time 5.000 Back Off! I just backed up maxclust.ndx to ./#maxclust.ndx.1# Total number of atoms in clusters = 13284 cmid: 1, cmax: 1, max_size: 13284 Back Off! I just backed up csize.xpm to ./#csize.xpm.1# --- Program: gmx clustsize, version 2016.5 Source file: src/gromacs/fileio/matio.cpp (line 690) Fatal error: Lo: 0.00, Mid: 1.00, Hi: 1.00 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Can any one help me out..what kind of error it is. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Young and Cheatham ions parameters for gromacs
Den 2019-05-15 kl. 08:12, skrev Harutyun Sahakyan: Dear GMX users I would like to use Young and Cheatham ions parameters ( https://pubs.acs.org/doi/full/10.1021/jp8001614#si1) with amber99sb-ildn. How can I convert sigma and epsilon values and use them with gromacs? For instance, I want to use K and Cl ions with scpe water, sigma (*R* min/2) and epsilon (ε) presented by Cheatham are in Å and kcal/mol. However, gromacs uses *nm *and *kJ/mol*, when I translated Å to nm and kcal to kJ and used that values I noticed some artifacts and unusual connections between K and Cl ions. What did I do wrong and what are the right parameters for K and Cl in this case? I suppose conversion from Å to nm is not correct, is sigma in gromacs *R* min/2 ? Before you use K+ please check Auffinger,P., Cheatham,T.E. and Vaiana,A.C. (2007) Spontaneous formation of KCl aggregates in biomolecular simulations: a force field issue? J. Chem. Theory Comput., 3, 1851–1859. My used parameters (nm and kJ/mol) K sigma 0.1593 epsilon 1.7978873936 Clsigma 0.2711 epsilon 0.05349244 in Young and Cheatham (Å and kcal/mol) K sigma 1.593 epsilon 0.4297054 Clsigma 2.711 epsilon 0.0127850 Thanks in advance, Harut -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] nmr distance restraints
0e+00) functype[1041]=DISRES, label= 3, type=1, low= 3.8403e-01, up1= 3.8403e-01, up2= 4.8829e-01, fac= 1.e+00) functype[1042]=DISRES, label= 4, type=1, low= 2.3397e-01, up1= 2.3397e-01, up2= 4.04900014e-01, fac= 1.e+00) functype[1043]=DISRES, label= 5, type=1, low= 2.3995e-01, up1= 2.3995e-01, up2= 4.06699985e-01, fac= 1.e+00) functype[1044]=DISRES, label= 6, type=1, low= 3.0303e-01, up1= 3.0303e-01, up2= 4.3502e-01, fac= 1.e+00) etc... Any suggestions about what is wrong here would be appreciated Thanks, Eiso -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] OPLS parameters for O2
Den 2019-05-10 kl. 00:42, skrev Shadi Fuladi: Hi, I'm trying to test molecular oxygen diffusion in electrolytes using OPLS force field. Is there any O2 parameters tested with OPLS AA forcefield? Thanks, SF There is a model described here Hub, J. S.; de Groot, B. L. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 1198−1203. that we have tested in the paper below and it has has quite accurate solubility in water. See Michiel van Lun, Jochen S. Hub, David van der Spoel and Inger Andersson: CO2 and O2 Distribution in Rubisco Suggests the Small Subunit Functions as a CO2 Reservoir J. Amer. Chem. Soc. 136 pp. 3165-3171 (2014) Cheers, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Implicit Solvent with User Defined Potentials
Den 2019-05-08 kl. 16:21, skrev Akash Banerjee: Dear Gromacs Developer, I want to use the implicit solvent (gbsa algorithm) along with User-defined tabulated potentials. Apparently, the implicit solvent option is not compatible with the vdw-type=USer option. Can I please get some advice on this? Thank you for your help. Kind regards, Akash GB has been removed from GROMACS and if old versions do not have this option it seems you are out of luck. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] How to calculate tetrahedral order parameter in GROMACS
Den 2019-05-07 kl. 14:34, skrev Soham Sarkar: Hello, I have two systems. One containing only water and the other one contains protein and water. Using g_select I made water in 1st solvation shell but the use of g_hydorder I cannot understand. I read the disscussion so far disscussed. For these two systems which index I need to choose, water or OW? What is the use of sgang1 and sgang2? Any suggestion is appreciated. Thanks and regards Soham The tool is not made for anything else than water I'm afraid. Please check this paper for details. Bjorn Steen Sæthre, Alex C. Hoffmann and David van der Spoel: Order parameters and algorithmic approaches for detection and demarcation of interfaces in hydrate-fluid and ice-fluid systems J. Chem. Theor. Comput. 10 pp. 5606-5616 (2014) -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] MW particle type in TIP4Pew
Den 2019-04-14 kl. 12:17, skrev Mandar Kulkarni: Hi, I am simulating protein using amber14sb with TIP4Pew water. I found that particle type for dummy mass MW in TIP4Pew is D in gromacs force field files and type A in user contributed version of amber14sb. Even acpype converted topology gives type A for MW. My understanding is that type D is correct for MW atomtype. but, I just want to make sure that before proceeding to production runs. Make that "V" for virtual site, but "D" for dummy is supported fro backwards compatibility. "A" is wrong as atoms should have a mass. Any suggestions will be helpful. Thanks in advance. Regards, Mandar Kulkarni -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Energy Conservation at the Beginning of a Production Run
Den 2019-03-28 kl. 21:19, skrev Kruse, Luke E.(MU-Student): In the mdout.mdp file corresponding to this run I have the line ; Do not constrain the start configuration continuation = no Do I need to change this to yes? Maybe, try a 100 step run where you save energies at each time step. Did you change anything else between minimization and production, e.g. constraint settings? The plot of energy vs time looks like an under damped response to a set point change in control theory - slight overshooting after the first few steps, then settling down to an average value nicely. This is what is leading me to believe that there is a large, non conservative force near the beginning that becomes smaller, and conservative. Time (ps) 0.00 -1851396.981075 0.10 -1851388.994856 0.20 -1851390.001591 0.30 -1851389.436699 0.40 -1851389.760231 0.50 -1851389.726310 0.60 -1851389.808428 0.70 -1851389.907829 0.80 -1851389.840644 0.90 -1851389.967373 1.00 -1851390.061502 1.10 -1851390.057500 1.20 -1851390.086172 1.30 -1851390.042747 1.40 -1851390.060210 1.50 -1851389.998599 1.60 -1851390.120319 1.70 -1851390.141846 1.80 -1851390.131003 1.90 -1851390.170220 2.00 -1851390.141617 2.10 -1851390.135779 2.20 -1851390.255565 2.30 -1851390.153947 2.40 -1851390.238681 2.50 -1851390.144512 2.60 -1851390.255200 2.633000 -1851390.178012 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of David van der Spoel Sent: Thursday, March 28, 2019 3:10:05 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Energy Conservation at the Beginning of a Production Run Den 2019-03-28 kl. 20:53, skrev Kruse, Luke E.(MU-Student): Hello gromacs users, I am trying to simulate a peptide amphiphile with the CHARMM27 force field. To do this I have had to specify an additional bond type and bond, angle, dihedral, etc. parameters in the .itp files of the force field. Then, to check if I had done this correctly, I minimized the system, and ran a production run to generate an NVE ensemble, so that I could make sure the system was conserving energy appropriately. After looking at the energy vs time plot (produces with the gmx energy command), however, the system jumps from an initial energy, up ~20 kJ per mole and then conserves energy for the most part (slight drifting but seems tolerable relative to the initial discontinuity). Is this discontinuity a normal happenstance or a result of bad minimization? Is that at step 0 in the simulation? Please check options like ; Do not constrain the start configuration continuation = no Thank you! Luke -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Energy Conservation at the Beginning of a Production Run
Den 2019-03-28 kl. 20:53, skrev Kruse, Luke E.(MU-Student): Hello gromacs users, I am trying to simulate a peptide amphiphile with the CHARMM27 force field. To do this I have had to specify an additional bond type and bond, angle, dihedral, etc. parameters in the .itp files of the force field. Then, to check if I had done this correctly, I minimized the system, and ran a production run to generate an NVE ensemble, so that I could make sure the system was conserving energy appropriately. After looking at the energy vs time plot (produces with the gmx energy command), however, the system jumps from an initial energy, up ~20 kJ per mole and then conserves energy for the most part (slight drifting but seems tolerable relative to the initial discontinuity). Is this discontinuity a normal happenstance or a result of bad minimization? Is that at step 0 in the simulation? Please check options like ; Do not constrain the start configuration continuation = no Thank you! Luke -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] All water molecules inside protein
Den 2019-02-03 kl. 11:09, skrev Dawid das: Dear Gromacs Users, I need to extract gro or pdb file with single snapshot from a trajectory for a protein inside solvation box. In the output, I need whole protein structure + all water molecules "inside" the protein. That could also mean all water molecules within let's say 0.3 nm distance from any atom belonging the protein. What is a simple and effective way to find only those water molecules which are within 0.3 nm distance from protein, please? Best wishes, Dawid Grabarek gmx trjorder -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] gmx covar and gmx anaeig
Den 2019-01-31 kl. 12:28, skrev Özge ENGİN: Hi All, I am working on 3 systems in parallel: 1) protein only, 2) protein+ligand1 and 3) protein+ligand2 using the same protein. Here, I want to get rmsf profiles of the systems along the first and second eigenvectors which can be get by gmx anaeig -rmsf option. I want to use the eigenvectors pertaining to protein only system and project the rest on to these eigenvectors to make a reasonable comparison. To do so, I used the following command lines: A) gmx covar on Protein_only trajectory B) gmx anaeig protein+ligand1 trajectory + eigenvectors of protein only what I get is similar rmsf profiles from A and B. Sure i am missing something but could not find. These are very crude methods that may or may not tell you anything about the systems under study. They are also strongly dependent on sampling. So your results means that A) you did long enough sampling as proved througn an independent method and there is little difference between the systems or B) your results are inconclusive. Thanks, Best, Ozge *Özge Şensoy, Ph.D.* Assistant Professor Department of Computer Engineering School of Engineering and Natural Sciences Istanbul Medipol University Kavacik Mah., Ekinciler Cad. No:19 34810 Beykoz, Istanbul e-mail: osen...@medipol.edu.tr Phone:+90 (216) 681-5100 <%280216%29%20681%2051%2000> (5621) <http://ipont.medipol.edu.tr/> -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04; upgraded with GTX1080TI
Den 2019-01-08 kl. 20:33, skrev Adarsh V. K.: Dear all, recently upgraded Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04 with a new GPU GTX1080TI. CUDA from 7.5 to 8. Driver 384. Problem: GPU not detected during MD run. Details are as follows: Try upgrading to gromacs 2019. 1) Running on 1 node with total 8 cores, 8 logical cores, 0 compatible GPUs Hardware detected: But deviceQuery as follows 2) ./deviceQuery ./deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) Detected 1 CUDA Capable device(s) Device 0: "GeForce GTX 1080 Ti" CUDA Driver Version / Runtime Version 9.0 / 8.0 CUDA Capability Major/Minor version number:6.1 Total amount of global memory: 11169 MBytes (11711807488 bytes) (28) Multiprocessors, (128) CUDA Cores/MP: 3584 CUDA Cores GPU Max Clock rate:1658 MHz (1.66 GHz) Memory Clock rate: 5505 Mhz Memory Bus Width: 352-bit L2 Cache Size: 2883584 bytes Maximum Texture Dimension Size (x,y,z) 1D=(131072), 2D=(131072, 65536), 3D=(16384, 16384, 16384) Maximum Layered 1D Texture Size, (num) layers 1D=(32768), 2048 layers Maximum Layered 2D Texture Size, (num) layers 2D=(32768, 32768), 2048 layers Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 49152 bytes Total number of registers available per block: 65536 Warp size: 32 Maximum number of threads per multiprocessor: 2048 Maximum number of threads per block: 1024 Max dimension size of a thread block (x,y,z): (1024, 1024, 64) Max dimension size of a grid size(x,y,z): (2147483647, 65535, 65535) Maximum memory pitch: 2147483647 bytes Texture alignment: 512 bytes Concurrent copy and kernel execution: Yes with 2 copy engine(s) Run time limit on kernels: Yes Integrated GPU sharing Host Memory:No Support host page-locked memory mapping: Yes Alignment requirement for Surfaces:Yes Device has ECC support:Disabled Device supports Unified Addressing (UVA): Yes Device PCI Domain ID / Bus ID / location ID: 0 / 1 / 0 Compute Mode: < Default (multiple host threads can use ::cudaSetDevice() with device simultaneously) > deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 9.0, CUDA Runtime Version = 8.0, NumDevs = 1, Device0 = GeForce GTX 1080 Ti Result = PASS -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] about 165 gromacs bug in the list
Den 2019-01-03 kl. 18:03, skrev Santosh Kumar Meena: Dear all, I would like to ask whether 165 gromacs bug in gromacs bug list related to non zero center of mass drift in Gromacs that became apparent only at long timescales is resolved in new versions. Thanks in advance. Regards Not that I know of. If you have a reproducible case please upload to the redmine issue. The problem has been to get just such a case. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Surface Energy calculation of polymeric materials
Den 2018-12-21 kl. 11:07, skrev Maria Luisa: Dear users, I did simulations with Gromacs on different polymeric materials in contact with salt solutions of NaCl. In particular I performed crystallization tests and now I'd like to find an energy parameter that could justify different behavior of systems studied in nucleation time and also in crystallization growth. What kind of calculation or command do you suggest to me? In particular I'd like to individuate an energy factor of polymeric surfaces, that implied changes in simulations. The surface tension of the solution may be somewhat useful, although this is an equilibrium property that may be hard to relate to activation energies that you are after. Note that nucleation time is also concentration dependent. Finally, vacuum/liquid surface tensions of salt solutions are difficult to get correct in simulations and the may need application of polarizable models. Maria Luisa Maria Luisa Perrotta Ph.D Student, CNR-ITM via P.Bucci, 87036 Rende (Cs) Italy email: ml.perro...@itm.cnr.it -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Mean square displacement on Log-Log plot?
Den 2018-12-10 kl. 21:57, skrev Kevin Boyd: Hi, If you're reporting a diffusion coefficient, they're probably looking for you to justify that you're out of the short-time subdiffusive regime. My experience is in bilayer simulations, where the MSD hits that regime typically in the time lag range of ~10-20 ns. For a qualitative estimate of whether you've reached the long timescale limit, you don't need a log-log plot, you can just eyeball when the MSD goes linear, and (again in my experience) that's generally sufficient. A log-log plot may make it easier to see, or catch some subtler trends. Maybe take a look at "Non-brownian diffusion in lipid membranes: experiments and simulations", by Metzler, Jeon, and Cherstvy, particularly some of the later figures look at the extent of subdiffusion with log-log plots. https://www.sciencedirect.com/science/article/pii/S0005273616300219 Thanks! Kevin On Mon, Dec 10, 2018 at 3:34 PM David van der Spoel wrote: Hi, unusual request, but here goes. I am dealing with a referee to one of my papers who is asking for a mean square displacement plots: "a log-log plot of the MSD vs. time, from which one could judge whether the long-time limit subject to multiple collisions and obstructions is actually reached." Any clue what the referee is looking for? References? Cheers, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.icm.uu.se&data=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541&sdata=wxcRUd55ynF4cbEOJVbKHbG%2BCeL6DAU8WlAbaG5wrQs%3D&reserved=0 -- Gromacs Users mailing list * Please search the archive at https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541&sdata=xs%2BZ9IA%2FzoeJPfpSIhIFZFF0kA624QnSyN1DqmVdaMk%3D&reserved=0 before posting! * Can't post? Read https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&data=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541&sdata=42CTt8iaJj2VC2RBUcz%2BI%2F%2BjU%2BKbX23srdKhAvuNBI4%3D&reserved=0 * For (un)subscribe requests visit https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541&sdata=oNjdubSZHzZqp4yN4Rezu4Trjl8cc9FDJMvEkkUmESQ%3D&reserved=0 or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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] Mean square displacement on Log-Log plot?
Hi, unusual request, but here goes. I am dealing with a referee to one of my papers who is asking for a mean square displacement plots: "a log-log plot of the MSD vs. time, from which one could judge whether the long-time limit subject to multiple collisions and obstructions is actually reached." Any clue what the referee is looking for? References? Cheers, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] [ implicit_genborn_params ] for Gromos54a7 FF
Den 2018-12-04 kl. 22:49, skrev Alex: Hi David, Thank you. On Tue, Dec 4, 2018 at 4:24 PM David van der Spoel wrote: Den 2018-12-04 kl. 21:58, skrev Alex: Dear all. I wonder where the [ implicit_genborn_params ] section should come in the below topol.top file for which the Gromos54a7 force fields are used? For the Amber and OPLS-FF I notice that all the [ implicit_genborn_params ] parameters are in a gbsa.itp file but that was not the case for Gromos54a7 and even it did not worked when I created a gbsa.itp for for gromos5a7. Please note first that only the 4.5 and 4.6 branches of gromacs run generalized born efficiently and reliably (as far as I know). I didn't know that, I use the 2018.2 version and at least the tpr file can be produced ... . Second, if there is no predefined force field you should not make an ad-hoc one but use a well-defined one instead. Third, why bother with generalized born at all? There are so many papers showing that the predictive power is poor that it will be hard to defend any results based on it. If non of Still, HCT and OBC, then what else you would suggest that has been implemented in Gromacs and could be used easily in Gromacs? I just wanted to see the diffusion and adsorption of some polymers to solid surface. The process is so slow in explicit water and I just wanted to see it the polymer come to the surface at all! However I see too much force in the slab with the current [ implicit_genborn_params ] parameter which I have used for now. For qualitative work it is fine, although there is basically no correlation between explicit solvent and implicit solvent for solvation energies (e.g. J. Chem. Theory Comput. 13 pp. 1034-1043 (2017)). This means that even if your polymer adsorbs to the surface, it may be unphysical. BTW, meanwhile I found that the [ implicit_genborn_params ] should come immediatly after the [ atomtypes ] section in topol.top file. Regards, Alex %-TOP--- #include "/u/alex/.local/gromos54a7.ff/forcefield.itp" ; #include "A.itp" #include "B.itp" #include "C.itp" ; [ system ] A-B-C in implicit water [ molecules ] A 1 B 29 C 14 B 29 C 14 %---------- Thank you Regards, Alex -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] [ implicit_genborn_params ] for Gromos54a7 FF
Den 2018-12-04 kl. 21:58, skrev Alex: Dear all. I wonder where the [ implicit_genborn_params ] section should come in the below topol.top file for which the Gromos54a7 force fields are used? For the Amber and OPLS-FF I notice that all the [ implicit_genborn_params ] parameters are in a gbsa.itp file but that was not the case for Gromos54a7 and even it did not worked when I created a gbsa.itp for for gromos5a7. Please note first that only the 4.5 and 4.6 branches of gromacs run generalized born efficiently and reliably (as far as I know). Second, if there is no predefined force field you should not make an ad-hoc one but use a well-defined one instead. Third, why bother with generalized born at all? There are so many papers showing that the predictive power is poor that it will be hard to defend any results based on it. %-TOP--- #include "/u/alex/.local/gromos54a7.ff/forcefield.itp" ; #include "A.itp" #include "B.itp" #include "C.itp" ; [ system ] A-B-C in implicit water [ molecules ] A 1 B 29 C 14 B 29 C 14 %-- Thank you Regards, Alex -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] g++ compiling with gromacs library
Den 2018-11-21 kl. 21:56, skrev Kit Sang Chu: Somehow the problem persists. Here I try -l /home/simon/Softs/gromacs5-1/opt/include again. What is in the directory /home/simon/Softs/gromacs5-1/opt/ It depends where you installed gromacs. By the way why use an ancient version of gromacs? g++ -l /home/simon/Softs/gromacs-5.1/opt/include GlyRot.cpp -o GlyRot.o -Wall -c GlyRot.cpp:8:10: fatal error: gromacs/commandline.h: No such file or directory #include "gromacs/commandline.h" ^~~ compilation terminated. Regards, Simon On Wed, Nov 21, 2018 at 12:18 PM Alexander Tzanov < alexander.tza...@csi.cuny.edu> wrote: Use -I/path to your include directory in CFLAGS. On Nov 21, 2018 2:59 PM, David van der Spoel wrote: Den 2018-11-21 kl. 19:09, skrev Kit Sang Chu: Hi everyone, I have a Makefile from my colleague and I am trying to make it compile. I have given the library path but the problem persists. g++ -I /home/simon/Softs/gromacs-5.1/opt GlyRot.cpp -o GlyRot.o -Wall -c -I /home/simon/Softs/gromacs-5.1/opt/include GlyRot.cpp:8:10: fatal error: gromacs/commandline.h: No such file or directory #include "gromacs/commandline.h" ^~~ compilation terminated. I understand it is a simple compile error. Still it would be great to know the answer here. Thanks in advance. Simon -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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. -- 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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] g++ compiling with gromacs library
Den 2018-11-21 kl. 19:09, skrev Kit Sang Chu: Hi everyone, I have a Makefile from my colleague and I am trying to make it compile. I have given the library path but the problem persists. g++ -I /home/simon/Softs/gromacs-5.1/opt GlyRot.cpp -o GlyRot.o -Wall -c -I /home/simon/Softs/gromacs-5.1/opt/include GlyRot.cpp:8:10: fatal error: gromacs/commandline.h: No such file or directory #include "gromacs/commandline.h" ^~~ compilation terminated. I understand it is a simple compile error. Still it would be great to know the answer here. Thanks in advance. Simon -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] multiple electric fields
Den 2018-10-28 kl. 00:47, skrev Alex: I would propose you add the constant in the code for now and work with it. If it works well please upload a redmine issues with a feture request. You literally have to add somewhere field = field + c check src/gromacs/applied_forces/electricfield.cpp Thanks for the file location, but this may turn into a bit of a nightmare, because that value of c would need to be varied in sweeps, so I suppose we will probably stick with LAMMPS for now. That said, of course, I would really like to request this feature either in the form of offset, or the ability to supply multiple statements for the same vector component. Alex The mdp file also hosts "user" variables in the inputrecord, see http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html If you set userreal1 in the mdp file to your desired value you can extract it in the code with some effort. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] Calculation chi angle for tryptophan residue
Den 2018-10-25 kl. 17:13, skrev Muhammad Harith Zulkifli: Hi, How can I plot a graph of chi angle of tryptohan residue over time from my trajectory file? What is the suitable command? gmx angle -type dihedral -h Thank you. Regards, Muhammad Harith bin Zulkifli Tel:013-9307882 E-mail: hzu...@gmail.com -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] multiple electric fields
Den 2018-10-26 kl. 07:46, skrev Alex: As expected, multiple instances of a given component are not accepted by Gromacs. Is there anything that can be done? Can the functional form be extended to the current form + constant offset? The use scenario is very simple: photosensitive solid-state ion channels. It is that relatively rare instance when there is no chemical reaction that results in photosensitivity, so one needs a constant driving field and an additional sinusoidal wave. We can set this up with LAMMPS, but our timescales will drop by a factor of five... Anyone? I would propose you add the constant in the code for now and work with it. If it works well please upload a redmine issues with a feture request. You literally have to add somewhere field = field + c check src/gromacs/applied_forces/electricfield.cpp Thanks, Alex On 10/25/2018 1:08 PM, Alex wrote: Hi all, Is it possible to have an electric field of the form described here: http://manual.gromacs.org/documentation/2018.1/user-guide/mdp-options.html#mdp-electric-field-x%20;%20electric-field-y%20;%20electric-field-z but with a constant component? In other words, for a given component (x,y, or z): E0_1 + E0_2*something-sinusoidal? For instance, can we have multiple 'electric-field-z' statements, each describing the desired portion? Thanks, Alex -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] GMX Helix Segmentation fault
Den 2018-10-16 kl. 11:14, skrev Budheswar Dehury: Dear All, Hello. I am doing analysis soem analysis of TM helix properties using the GMX helix tool of GROMACS 2018.2. Though, in someways its working in the old version 2016.2 but its not working in the latest 2018.2 version. I have appended the following error. If this is reproducible please make a small test system and upload a bug report at https://redmine.gromacs.org gmx helix -f ../md.xtc -s ../md.tpr -n index.ndx Reading file ../md.tpr, VERSION 2018.2 (single precision) Reading frame 0 time 20.000 Please select a group containing the entire backbone Group 0 ( System) has 201382 elements Group 1 (Protein) has 22327 elements Group 2 ( Protein-H) has 11159 elements Group 3 (C-alpha) has 1414 elements Group 4 ( Backbone) has 4242 elements Group 5 ( MainChain) has 5651 elements Group 6 ( MainChain+Cb) has 6978 elements Group 7 (MainChain+H) has 6986 elements Group 8 ( SideChain) has 15341 elements Group 9 (SideChain-H) has 5508 elements Group10 (Prot-Masses) has 22327 elements Group11 (non-Protein) has 179055 elements Group12 ( Other) has 179055 elements Group13 ( POPC) has 40468 elements Group14 ( TIP3) has 138315 elements Group15 (SOD) has 146 elements Group16 (CLA) has 126 elements Group17 ( a_10743-11091) has 349 elements Select a group: 17 Selected 17: 'a_10743-11091' Checking group a_10743-11091 There are 21 residues There are 19 complete backbone residues (from 2 to 20) nall=349 Reading file ../md.tpr, VERSION 2018.2 (single precision) Please help me to rectify this error or suggest any idea how should I get reed of this. Thanking you With Warm Regards Budheswar -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
Re: [gmx-users] simulation in acidic condition
== -- 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. -- 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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
