Re: [gmx-users] Criteria and Energy Conservation
Well, yeah. But I want to look at the HOMO-LUMO gap of the system in the living environment. Since the system is too big to do MD with the QM code, I tried to use the best force field description I could, and the smallest box as well, to get structures that could represent the system at 300K. And the forces from QM are not so bad so far, within the order I'd expect from MD with the QM code. Anyway, thanks very much for the hints so far, David, and if you have some suggestion or anything at all to add, feel free to do so. > [EMAIL PROTECTED] wrote: > > Thank you very much again, David! Then it's fine for me, since what I want > to > > do is a single point QM in "termalized" snapshots of the dynamics and not > QM > > minimization. > But then you will get systematically incorrect energies due to weird > (force field dependent) bond lengths etc. > > > > Gustavo > > > >> [EMAIL PROTECTED] wrote: > >>> Dear GROMACS Users, > >>> > >>> I'm trying to use GROMACS to get some MD snapshots for single-point > >> quantum > >>> mechanical calculations, trying to observe HOMO-LUMO gap of a protein > >> immersed > >>> in water with counterions, at a given salt concentration (4600 atoms in > >> total). > >>> I'd like to know if they are reliable enough to send to QM calculations. > >> I've > >>> got two questions: Which are the criteria I should be looking at? And one > >> of > >>> them I've analyzed was energy conservation (I'm doing 300K NVT MD, with > 10A > >>> cutoff for vdw and coulomb, with PME electrostatics, and double > precision), > >> and > >>> the manual says a Ekin RMSD/Tot Energy RMSD ratio below 0.05 is fine, but > >> I've > >>> got 0.3-0.5 in all simulations I've done. What should I do? > >>> > >> This is because of T coupling. If you turn off T coupling it will be > >> better (but you will not have constant T, and the energy will dirft in > >> the long run). Your starting structures are fine for QM, but QM > >> minimization will take a LONG time. > >> > >> > >>> Thanks in advance, > >>> > >>> Gustavo Troiano Feliciano > >>> > >>> > >>> > >>> This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. > >>> ___ > >>> gmx-users mailing listgmx-users@gromacs.org > >>> http://www.gromacs.org/mailman/listinfo/gmx-users > >>> Please search the archive at http://www.gromacs.org/search before > posting! > >>> Please don't post (un)subscribe requests to the list. Use the > >>> www interface or send it to [EMAIL PROTECTED] > >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > >> -- > >> David van der Spoel, Ph.D. > >> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > >> [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > >> ___ > >> gmx-users mailing listgmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > > > > > > > > > > > This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David. > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. _
Re: [gmx-users] Criteria and Energy Conservation
Thank you very much again, David! Then it's fine for me, since what I want to do is a single point QM in "termalized" snapshots of the dynamics and not QM minimization. Gustavo > [EMAIL PROTECTED] wrote: > > Dear GROMACS Users, > > > > I'm trying to use GROMACS to get some MD snapshots for single-point > quantum > > mechanical calculations, trying to observe HOMO-LUMO gap of a protein > immersed > > in water with counterions, at a given salt concentration (4600 atoms in > total). > > I'd like to know if they are reliable enough to send to QM calculations. > I've > > got two questions: Which are the criteria I should be looking at? And one > of > > them I've analyzed was energy conservation (I'm doing 300K NVT MD, with 10A > > cutoff for vdw and coulomb, with PME electrostatics, and double precision), > and > > the manual says a Ekin RMSD/Tot Energy RMSD ratio below 0.05 is fine, but > I've > > got 0.3-0.5 in all simulations I've done. What should I do? > > > This is because of T coupling. If you turn off T coupling it will be > better (but you will not have constant T, and the energy will dirft in > the long run). Your starting structures are fine for QM, but QM > minimization will take a LONG time. > > > > Thanks in advance, > > > > Gustavo Troiano Feliciano > > > > > > > > This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Criteria and Energy Conservation
Dear GROMACS Users, I'm trying to use GROMACS to get some MD snapshots for single-point quantum mechanical calculations, trying to observe HOMO-LUMO gap of a protein immersed in water with counterions, at a given salt concentration (4600 atoms in total). I'd like to know if they are reliable enough to send to QM calculations. I've got two questions: Which are the criteria I should be looking at? And one of them I've analyzed was energy conservation (I'm doing 300K NVT MD, with 10A cutoff for vdw and coulomb, with PME electrostatics, and double precision), and the manual says a Ekin RMSD/Tot Energy RMSD ratio below 0.05 is fine, but I've got 0.3-0.5 in all simulations I've done. What should I do? Thanks in advance, Gustavo Troiano Feliciano This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Protein coming out of the box
Hi all I'm simulating a helical protein in a water box, neutralized with Na and Cl to a 0.2M comcentration. I had to pick the smallest box I could (in editconf, rectangular, with -d 0.1, and -princ to align the box with the helix). But in the MD trajectory I see the protein coming out of the box, most of the time. I know that it uses PBC, and I'm seeing just 1 image, but does it mean that there's something wrong with the MD? Thanks in advance, Gustavo This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Alpha-Helix Dipole
Hi David, I tried to use the option -mutot in g_energy, but all I get is the component dipoles. They match what I've got in the file Mtot.xvg from g_dipoles, which is really high (for all the system: water+ polyala helix, fluctuates between 100 and 300 D), but in adip.xvg (the average) the value in each time is very low (around 2.3 D). The index file contains only the standard options (protein, SOL, backbone, etc..) and when I try to select backbone (e.g. in g_dipoles) it gives the fatal error: "The index group is not a set of whole molecules". Why is the Mtot like this and what exactly does the average mean? Anyway, thanks for all the guidance, it helped a lot! I tried to make it objective now and this is the last question I send you, for not wasting your time! If I can't conclude anything, can you send me any reference, or some exercises which I could compare some results and see if what I'm doing is right or what to expect from the dipole calculation? (I think that the structures are ok for the QM, but just I wanted to confirm if that situation is the closest that we have for the helix in water) Thank you very much (sorry if any of the questions seemed stupid!) Gustavo > [EMAIL PROTECTED] wrote: > > Just one more thing, David. I read the manual, but I couldn't realize: is > the > > average dipole, (at the top of the g_dipoles output) the overall dipole of > the > > system? (also in the adip.xvg, plotted against time). Because all I want to > > know is whether the system has a low dipole moment (which in the case of > > polyala+h2o, the average is 2.3 D) > > > > depends on your index file. the total dipole is also stored in the > energy file, so you can run g_energy to get it out, or g_dipoles -enx to > compute dielectric constants etc. > > > Gustavo > > > > > >> [EMAIL PROTECTED] wrote: > >>> Hi David > >>> > >>> Thank you very much for the reply! So, which group, in the end, shall I > >> select > >>> in g_dipoles to see the dipole? And how to use trjconv after editconf the > >> way > >>> you told me? (the input/output of editconf is a .gro file and of trjconv > is > >>> .trr/.xtc files) And whose group shall I select in the least > squares/output > >>> prompts in trjconv -fit trans+rot? > >>> > >>> Thank you very much, > >>> Gustavo > >>> > >>> > >> I would do both the helix backbone, and the entire helix, so that you > >> can test whether the sidechains compensate for the net dipole or the > >> other way around. You could also look at the net dipole of the water > >> with resect to the helix. > >> > >> As for trjconv, please read the manual about aligning structures > >> (trjconv -h) > >> > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > >> > >> -- > >> David van der Spoel, Ph.D. > >> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > >> [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > >> ___ > >> gmx-users mailing listgmx-users@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > > > > > > > > > > > This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at ht
Re: [gmx-users] Alpha-Helix Dipole
Just one more thing, David. I read the manual, but I couldn't realize: is the average dipole, (at the top of the g_dipoles output) the overall dipole of the system? (also in the adip.xvg, plotted against time). Because all I want to know is whether the system has a low dipole moment (which in the case of polyala+h2o, the average is 2.3 D) Gustavo > [EMAIL PROTECTED] wrote: > > Hi David > > > > Thank you very much for the reply! So, which group, in the end, shall I > select > > in g_dipoles to see the dipole? And how to use trjconv after editconf the > way > > you told me? (the input/output of editconf is a .gro file and of trjconv is > > .trr/.xtc files) And whose group shall I select in the least squares/output > > prompts in trjconv -fit trans+rot? > > > > Thank you very much, > > Gustavo > > > > > I would do both the helix backbone, and the entire helix, so that you > can test whether the sidechains compensate for the net dipole or the > other way around. You could also look at the net dipole of the water > with resect to the helix. > > As for trjconv, please read the manual about aligning structures > (trjconv -h) > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Alpha-Helix Dipole
Thank you for the guidance, David. Now I got it, but a thing that also helped was to set the option -pbc inbox in trjconv, which I didn't know if I had to (I read the manual, but even so, I didn't know). Now I see the water dipole counterbalances the entire protein one (I was testing in PolyALA, so no effect of the residues. Now I'll test in my helix) Thank you again, Gustavo > [EMAIL PROTECTED] wrote: > > Hi David > > > > Thank you very much for the reply! So, which group, in the end, shall I > select > > in g_dipoles to see the dipole? And how to use trjconv after editconf the > way > > you told me? (the input/output of editconf is a .gro file and of trjconv is > > .trr/.xtc files) And whose group shall I select in the least squares/output > > prompts in trjconv -fit trans+rot? > > > > Thank you very much, > > Gustavo > > > > > I would do both the helix backbone, and the entire helix, so that you > can test whether the sidechains compensate for the net dipole or the > other way around. You could also look at the net dipole of the water > with resect to the helix. > > As for trjconv, please read the manual about aligning structures > (trjconv -h) > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Alpha-Helix Dipole
Hi David Thank you very much for the reply! So, which group, in the end, shall I select in g_dipoles to see the dipole? And how to use trjconv after editconf the way you told me? (the input/output of editconf is a .gro file and of trjconv is .trr/.xtc files) And whose group shall I select in the least squares/output prompts in trjconv -fit trans+rot? Thank you very much, Gustavo > [EMAIL PROTECTED] wrote: > > Hello > > > > I'm a beginner user of GROMACS, and I'm currently trying to simulate some > alpha > > helices in an explicit water box to extract some initial structures for > > subsequent quantum mechanical calculations (which uses pbc as well). I'd > like > > to know if there's a way to check if the dipole moment of the protein > backbone > > is screened by the water, the way it should be, because if not, the results > > from QM will be incorrect for what I want to observe. I checked the results > > with g_dipoles_d and below is what I got, for 500ps 300K NVT MD of a 20 > residue > > polyalanine in a box of 1813 water molecules (total of 5651 atoms, 1nm > from the > > edges of the helix), but I'm not certain where to look to decide if it's > correct > > (of course, a frame won't necessarily have a zero dipole moment, but maybe > it > > seems too high? If you look at the Mtot.xvg, the total dipole is between > 240 > > and 60 Debye). Any help would be appreciated! > > > did you select just the helix backbone for this calculation? probably > not, and then you are looking at the water. in addition you probably > want to align the helix to the box otherwise you are looking at the > average of a moving helix. editconf -princ and then use trjconv -fit > rot+trans to fit the trajectory on the first structure. > > > Thanks in advance, > > Gustavo > > > > > > Dipole moment (Debye) > > - > > Average = 2.3041 Std. Dev. = 1.2691 Error = 0.0042 > > > > The following averages for the complete trajectory have been calculated: > > > > Total < M_x > = 39.2483 Debye > > Total < M_y > = -54.7993 Debye > > Total < M_z > = 59.1645 Debye > > > > Total < M_x^2 > = 9509.68 Debye^2 > > Total < M_y^2 > = 14277.5 Debye^2 > > Total < M_z^2 > = 17721.9 Debye^2 > > > > Total < |M|^2 > = 41509.1 Debye^2 > > Total < |M| >^2 = 8043.83 Debye^2 > > > > < |M|^2 > - < |M| >^2 = 33465.3 Debye^2 > > > > > > > > > > This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Alpha-Helix Dipole
Hello I'm a beginner user of GROMACS, and I'm currently trying to simulate some alpha helices in an explicit water box to extract some initial structures for subsequent quantum mechanical calculations (which uses pbc as well). I'd like to know if there's a way to check if the dipole moment of the protein backbone is screened by the water, the way it should be, because if not, the results from QM will be incorrect for what I want to observe. I checked the results with g_dipoles_d and below is what I got, for 500ps 300K NVT MD of a 20 residue polyalanine in a box of 1813 water molecules (total of 5651 atoms, 1nm from the edges of the helix), but I'm not certain where to look to decide if it's correct (of course, a frame won't necessarily have a zero dipole moment, but maybe it seems too high? If you look at the Mtot.xvg, the total dipole is between 240 and 60 Debye). Any help would be appreciated! Thanks in advance, Gustavo Dipole moment (Debye) - Average = 2.3041 Std. Dev. = 1.2691 Error = 0.0042 The following averages for the complete trajectory have been calculated: Total < M_x > = 39.2483 Debye Total < M_y > = -54.7993 Debye Total < M_z > = 59.1645 Debye Total < M_x^2 > = 9509.68 Debye^2 Total < M_y^2 > = 14277.5 Debye^2 Total < M_z^2 > = 17721.9 Debye^2 Total < |M|^2 > = 41509.1 Debye^2 Total < |M| >^2 = 8043.83 Debye^2 < |M|^2 > - < |M| >^2 = 33465.3 Debye^2 This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
