[gmx-users] inconsistent shifts while using distance restraints
Dear gmx-useres, I am simulating a protein in a box with water and ions and now I am trying to keep the ions away from a particular residue of the protein. To do this I am using distance restraints. So I created a new molecule type with the protein and all ions and added distance restraints between each ion and the C-alpha of the residue in the protein. To get a repulsive flat-bottom distance restraint I set low to 0.9 nm and up1,up2 to 98, 99nm (box vectors are all around 15nm). Everything seems to be working fine (in some 3000steps test simulations) but mdrun prints the message "There were inconsistent shifts." I guess this is because I have distance restraints between atoms that are further away from each other than half the shortest box vector, but since there is no force acting on those pairs I would not worry too much. So my questions are: Is my guess correct? Is there a better way than distance restraints too keep the ions away from their binding site? Here I have to add that the protein is actually a dimer so I have two distance restraints per ion, that is the reason to choose distance restraints rather than position restraints. cheers, Daniel Kortzak Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] strange behaviout in 5.1.2
Dear All, when using gmx-5.1.2 with a mdp file with the following pressure coupling parameters: ; pressure coupling Pcoupl = berendsen Pcoupltype = semiisotropic nstpcouple = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 5 5 compressibility = 4.5e-5 4.5e-5 ref_p= 1.0 1.0 ; Scaling of reference coordinates, No, All or COM refcoord_scaling = all grompp gives the error message: ERROR 1 [file parameter.mdp, line 387]: Right hand side '5 5' for parameter 'tau_p' in parameter file is not a real value With versions below 5.1.2 everything seems to be fine. Are there additional changes beyond what is mentioned in the release notes or am I to blind to find the right section? Best, Daniel Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] Regression test for mdrun only installation
Dear GMX-Users, just one quick question: is there a simple way to do the regression test with a mdrun-only build of gromacs 5.05? cheers, Daniel Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_wham error in umbrella simulation
Maybe some empty lines at the end of your .dat files. Dear all, I am doing an umbrella simulation, and come across the following error. Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 Found 27 tpr and 27 pull force files in tpr-files.dat and pullf-files.dat, respectively Reading 13 tpr and pullf files Automatic determination of boundaries... --- Program g_wham, VERSION 5.0.4 Source code file: /home/tm/Downloads/gromacs/src/gromacs/gmxana/gmx_wham.cpp, line: 1767 Fatal error: . Should be tpr, xvg, or pdo.0.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors tpr-files.dat: umbrella0.tpr umbrella137.tpr umbrella155.tpr umbrella163.tpr umbrella169.tpr umbrella174.tpr umbrella179.tpr umbrella185.tpr umbrella199.tpr umbrella206.tpr umbrella223.tpr umbrella239.tpr umbrella257.tpr umbrella275.tpr umbrella291.tpr umbrella308.tpr umbrella324.tpr umbrella344.tpr umbrella369.tpr umbrella383.tpr umbrella392.tpr umbrella422.tpr umbrella450.tpr umbrella463.tpr umbrella479.tpr umbrella497.tpr umbrella499.tpr pullf-files.dat pullf0.xvg pullf137.xvg pullf155.xvg pullf163.xvg pullf169.xvg pullf174.xvg pullf179.xvg pullf185.xvg pullf199.xvg pullf206.xvg pullf223.xvg pullf239.xvg pullf257.xvg pullf275.xvg pullf291.xvg pullf308.xvg pullf324.xvg pullf344.xvg pullf369.xvg pullf383.xvg pullf392.xvg pullf422.xvg pullf450.xvg pullf463.xvg pullf479.xvg pullf497.xvg pullf499.xvg I used this method several times before, and did not come across this problem. could anybody tell me where is the problem? Thanks Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] Variable force constant in umbrella sampling
Dear gromacs users, I have again some question regarding umbrella sampling. Is it ok to use different force constants in the different umbrella runs? So far I only read papers where they keep it constant but for me it could be useful to vary this along the reactioncoordinate. Best, Daniel Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] Variable force constant in umbrella sampling
Dear Chris, thanks for this information. What you describe is exactly the situation I ran into. I have a very sharp maximum close to the binding site which is not sampled well with a weak force while in bulk the weak force looks fine. Daniel Dear Daniel: It is perfectly fine to use different force constants for different umbrellas. This is commonly done, for example, when you have a very sharp maximum in your PMF and you need to place a few umbrellas at and near this maximum with very strong force constants in order to get good sampling. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Kortzak, Daniel d.kort...@fz-juelich.de Sent: 12 February 2015 22:58 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Variable force constant in umbrella sampling Dear gromacs users, I have again some question regarding umbrella sampling. Is it ok to use different force constants in the different umbrella runs? So far I only read papers where they keep it constant but for me it could be useful to vary this along the reactioncoordinate. Best, Daniel Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] Free energy calculations with pull code and umbrella sampling
Hi All, I have one quick questions about free energy calculations via pull code+umbrella sampling. (see below for some further information on what I am trying) First of all I think Justin is right umbrella sampling is much more straightforward. In particular in my situation where I see spontaneous binding at the site I am interested in, i.e. I already have a pathway of the ion to the binding site. So what I would do now is: Skip the pull code and just use the pathway I already have for the umbrella sampling. Again my question is: Is this sensible? Of course I have to check if the spacing of the pathway is close enough (output frequency of the xtc was 10ps) but on first sight I think it is, I could easily construct ~30 intermediates from the data I already have. If I need more intermediates my approach would be to use frames I already have and only pull between the positions of those frames instead of pulling the whole way from the binding site to the bulk. On 2/5/15 6:59 AM, Kortzak, Daniel wrote: Dear All, I want to calculate the free energy of binding of a single sodium ion to a protein. I want to do this by decoupling the ion in the binding site (with the couple-moltype approach). The work-flow I have in mind is roughly: 1. Start with ion in binding site 2. Turn on position restraints (since this only one atom I don't have to care about orientation etc.) 3. Decouple (And do the same for a ion in bulk solution in another simulation.) First of all is this sensible or are there better ways of doing this? Wouldn't just using the pull code to do umbrella sampling be a much more straightforward approach? You don't have to deal with compensating for artifacts associated with the restraint potential during decoupling and removing a charge from the system. -Justin Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] Position restraints and free energy calculations
Wouldn't just using the pull code to do umbrella sampling be a much more straightforward approach? You don't have to deal with compensating for artifacts associated with the restraint potential during decoupling and removing a charge from the system. -Justin Hi Justin, thanks for your fast reply. So far I did not consider this because on alchemistry.org they say beginners should start with the decoupling approach and all the papers I read so far also do only the decoupling approach (even in the simple case of a single ion binding to a protein). But of course this is no reason why I should not try the pulling. One real problem might be that the binding site is buried relatively deep in the protein. First I have to read a little more but soon I will be back with questions regarding the pulling method :) Nevertheless I am still wondering about the other questions I asked (just curiosity, maybe I at some point this will be important for me). Daniel Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] Position restraints and free energy calculations
Dear All, I want to calculate the free energy of binding of a single sodium ion to a protein. I want to do this by decoupling the ion in the binding site (with the couple-moltype approach). The work-flow I have in mind is roughly: 1. Start with ion in binding site 2. Turn on position restraints (since this only one atom I don't have to care about orientation etc.) 3. Decouple (And do the same for a ion in bulk solution in another simulation.) First of all is this sensible or are there better ways of doing this? Can I do 2. by normal position restraints in my topology or do I have to use a pull code? The former would be more easy to execute but the manual entry for the restraint-lambdas sounds like I have to do the latter. A more precise version of my question would be: Has the decoupling/annihilating procedure (in particular the value of the restraint-lambda) any effect on the position restraints defined in the [moleculetype] section of the decoupled molecule? Then another thing is, that it would be more convenient (convenient for me because I need less jobs in the queue I am not claiming that this would be more efficient) to do both decoupling of an ion in the protein and coupling another ion in solution in the same simulation. But as far as I understand the couple-moltype approach, I can only decouple an ion in protein and decouple another ion in solution which would give useless results if do this in the same simulation. The only solution to this I see, is to introduce dummy atoms and use the A-B-topology approach. Is this correct? Best regards and thanks in advance for reading, Daniel Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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.
