Re: [gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC
On 12/10/11 3:23 AM, Matthew Zwier wrote: Hi Ruhollah, A while ago on the list there was a discussion of extreme memory use and possibly-incorrect results from g_msd under some conditions. The problem could be worked around by imaging the trajectory with trjconv first to remove jumps across the box, then running g_msd on the results. Perhaps you'll have some more success with that workflow. All of this is not necessary. You should first try to do more tests before you claim a bug. For instance, compute the msd of a single Ca atom. Furthermore you do not state how your simulation was done and how long it was. Since you have a single molecule statistics will be poor unless you simulate for 100 ns or so. Cheers, Matt Z. On Fri, Dec 9, 2011 at 6:30 PM, Ruhollah Moussavi-Baygi ruhollah...@gmail.com wrote: David, thank you for your reply. but, g_msd gives a diffusion coefficient which is one order of magnitude higher than expected for a small polypeptide (15 res long with gyration Rg ~ 0.8nm) with the same size. this is command line i used: g_msd-mpi -f md_mine_2nd.xtc -s md_mine_2nd.tpr -o msd_2nd.xvg when visualizing, I can see that the polypeptide crosses the boundary several times. apparently, g_msd counts these 'artificial' jumps in MSD calculation. and, that's probably why the diffusion coefficient is calculated such high (i.e. 500 um2/s for a small protein). if this is the case, it is a bug in g_msd I believe. is there any way to get round this problem? -- Forwarded message -- From: Anonymousros...@kth.se Date: Fri, Dec 9, 2011 at 12:17 AM Subject: Comment for Forum topic: diffusion coefficient To: ruhollah...@gmail.com Hi ruhollahmoussavi-baygi, Comment by davidvanderspoel: diffusion coefficient On 2011-12-09 08:34, Mark Abraham wrote: On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote: I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant [1]) because of periodic boundary condition, when the peptide goes out of the right side it comes in from left side, which leads to an artificial displacement. this will give rise to a non-realistic MSD. is g_msd intelligent enough to avoid this artificial displacement? Yes it is. Not sure about g_msd, but you can take care of it yourself with a workflow derived from the information here http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Condi... [2] Mark Read more http://support.scalalife.eu/content/diffusion-coefficient#comment-103 -- This is an automatic message from ScalaLife To manage your subscriptions, browse to http://support.scalalife.eu/user/291/notifications You can unsubscribe at http://support.scalalife.eu/notifications/unsubscribe/sid/131?signature=c1e841f7c725c82291ca5d3191044f3c [1] http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant [2] http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -- Best, Ruhollah Moussavi-Baygi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David. David van der Spoel, PhD, Professor of Biology 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 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC
David, thank you for your reply. but, g_msd gives a diffusion coefficient which is one order of magnitude higher than expected for a small polypeptide (15 res long with gyration Rg ~ 0.8nm) with the same size. this is command line i used: g_msd-mpi -f md_mine_2nd.xtc -s md_mine_2nd.tpr -o msd_2nd.xvg when visualizing, I can see that the polypeptide crosses the boundary several times. apparently, g_msd counts these 'artificial' jumps in MSD calculation. and, that's probably why the diffusion coefficient is calculated such high (i.e. 500 um2/s for a small protein). if this is the case, it is a bug in g_msd I believe. is there any way to get round this problem? -- Forwarded message -- From: Anonymous ros...@kth.se Date: Fri, Dec 9, 2011 at 12:17 AM Subject: Comment for Forum topic: diffusion coefficient To: ruhollah...@gmail.com Hi ruhollahmoussavi-baygi, Comment by davidvanderspoel: diffusion coefficient On 2011-12-09 08:34, Mark Abraham wrote: On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote: I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/**Documentation/How-tos/**Diffusion_Constanthttp://www.gromacs.org/Documentation/How-tos/Diffusion_Constant[1]) because of periodic boundary condition, when the peptide goes out of the right side it comes in from left side, which leads to an artificial displacement. this will give rise to a non-realistic MSD. is g_msd intelligent enough to avoid this artificial displacement? Yes it is. Not sure about g_msd, but you can take care of it yourself with a workflow derived from the information here http://www.gromacs.org/**Documentation/Terminology/** Periodic_Boundary_Condi.http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Condi... [2] Mark Read more http://support.scalalife.eu/**content/diffusion-coefficient#** comment-103http://support.scalalife.eu/content/diffusion-coefficient#comment-103 -- This is an automatic message from ScalaLife To manage your subscriptions, browse to http://support.scalalife.eu/**user/291/notificationshttp://support.scalalife.eu/user/291/notificationsYou can unsubscribe at http://support.scalalife.eu/**notifications/unsubscribe/sid/**131?signature= **c1e841f7c725c82291ca5d3191044f**3chttp://support.scalalife.eu/notifications/unsubscribe/sid/131?signature=c1e841f7c725c82291ca5d3191044f3c [1] http://www.gromacs.org/**Documentation/How-tos/**Diffusion_Constanthttp://www.gromacs.org/Documentation/How-tos/Diffusion_Constant [2] http://www.gromacs.org/**Documentation/Terminology/** Periodic_Boundary_Conditionshttp://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -- Best, Ruhollah Moussavi-Baygi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC
Hi Ruhollah, A while ago on the list there was a discussion of extreme memory use and possibly-incorrect results from g_msd under some conditions. The problem could be worked around by imaging the trajectory with trjconv first to remove jumps across the box, then running g_msd on the results. Perhaps you'll have some more success with that workflow. Cheers, Matt Z. On Fri, Dec 9, 2011 at 6:30 PM, Ruhollah Moussavi-Baygi ruhollah...@gmail.com wrote: David, thank you for your reply. but, g_msd gives a diffusion coefficient which is one order of magnitude higher than expected for a small polypeptide (15 res long with gyration Rg ~ 0.8nm) with the same size. this is command line i used: g_msd-mpi -f md_mine_2nd.xtc -s md_mine_2nd.tpr -o msd_2nd.xvg when visualizing, I can see that the polypeptide crosses the boundary several times. apparently, g_msd counts these 'artificial' jumps in MSD calculation. and, that's probably why the diffusion coefficient is calculated such high (i.e. 500 um2/s for a small protein). if this is the case, it is a bug in g_msd I believe. is there any way to get round this problem? -- Forwarded message -- From: Anonymous ros...@kth.se Date: Fri, Dec 9, 2011 at 12:17 AM Subject: Comment for Forum topic: diffusion coefficient To: ruhollah...@gmail.com Hi ruhollahmoussavi-baygi, Comment by davidvanderspoel: diffusion coefficient On 2011-12-09 08:34, Mark Abraham wrote: On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote: I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant [1]) because of periodic boundary condition, when the peptide goes out of the right side it comes in from left side, which leads to an artificial displacement. this will give rise to a non-realistic MSD. is g_msd intelligent enough to avoid this artificial displacement? Yes it is. Not sure about g_msd, but you can take care of it yourself with a workflow derived from the information here http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Condi... [2] Mark Read more http://support.scalalife.eu/content/diffusion-coefficient#comment-103 -- This is an automatic message from ScalaLife To manage your subscriptions, browse to http://support.scalalife.eu/user/291/notifications You can unsubscribe at http://support.scalalife.eu/notifications/unsubscribe/sid/131?signature=c1e841f7c725c82291ca5d3191044f3c [1] http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant [2] http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -- Best, Ruhollah Moussavi-Baygi -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] diffusion coefficient
I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant) because of periodic boundary condition, when the peptide goes out of the right side it comes in from left side, which leads to an artificial displacement. this will give rise to a non-realistic MSD. is g_msd intelligent enough to avoid this artificial displacement? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] diffusion coefficient
On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote: I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant) because of periodic boundary condition, when the peptide goes out of the right side it comes in from left side, which leads to an artificial displacement. this will give rise to a non-realistic MSD. is g_msd intelligent enough to avoid this artificial displacement? Not sure about g_msd, but you can take care of it yourself with a workflow derived from the information here http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] diffusion coefficient
On 2011-12-09 08:34, Mark Abraham wrote: On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote: I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant) because of periodic boundary condition, when the peptide goes out of the right side it comes in from left side, which leads to an artificial displacement. this will give rise to a non-realistic MSD. is g_msd intelligent enough to avoid this artificial displacement? Yes it is. Not sure about g_msd, but you can take care of it yourself with a workflow derived from the information here http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Diffusion Coefficient
Hi I calculated the diffusion coefficient for lysozyme and get ~4x1e-6 (cm2/s) But, the experimental data is around 1x1e-6 (cm2/s). How could I explain for this discrepency? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Diffusion Coefficient
Chih-Ying Lin wrote: Hi I calculated the diffusion coefficient for lysozyme and get ~4x1e-6 (cm2/s) But, the experimental data is around 1x1e-6 (cm2/s). How could I explain for this discrepency? If the simulation is based off of a simulation of a single lysozyme protein in water, I'd be amazed at such good agreement. -Justin Thank you Lin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] diffusion coefficient of oxygen
Respected Experts I need your help In my study of diffusion of a oxygen molecule in 255 molecules of water, I previously used SPC water model with ffgmx force field with cutoff L-J and Coulomb interaction. I wanted to reproduce the experimental value 2.4 unit for diffusion coefficient of oxygen in water at 298 K and 1 atm. To equilibrate the system to the experimental water density of 997 I used Berendsen thermostat and the same barostat. The density of the system was 980(+-) 10 kg/m3 which is not the experimental value. After equilibration, I subjected the system to NVT ensemble md of 100 ns. I got the msd for oxygen molecule and analyzing first 4 ns (which was a st line part) of the plot, I got the diffusion coefficient of about 2.45 unit which is close to the experimental value. The question is how can the diffusion coefficient be so close when density is not produced. Is this a mere coincidence? Thinking that I used TIP4P water model with the same number but different force field ffG3a . I equilibrated the system to the same pressure and temperature with the same algorithms. After equilibration, the correspondng density was 991(+-) 15 kg/m3. Then I subjected it to the production run of 100ns. Now what I see is that the MSD curve is a hill, initially increasing, reaching maximum and again returning to the base. The diffusion coefficient is 0.7 unit for 100 ns of trajectory. What would have happened? Is this due to the increased density? Your precious knowledge on the subject matter would give me a sigh of relief. Looking forward to hearing from you neal -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] diffusion coefficient of oxygen
Sunil Thapa wrote: Respected Experts I need your help In my study of diffusion of a oxygen molecule in 255 molecules of water, I previously used SPC water model with ffgmx force field with cutoff L-J and Coulomb interaction. I wanted to reproduce the experimental value 2.4 unit for diffusion coefficient of oxygen in water at 298 K and 1 atm. To equilibrate the system to the experimental water density of 997 I used Berendsen thermostat and the same barostat. The density of the system was 980(+-) 10 kg/m3 which is not the experimental value. After equilibration, I subjected the system to NVT ensemble md of 100 ns. I got the msd for oxygen molecule and analyzing first 4 ns (which was a st line part) of the plot, I got the diffusion coefficient of about 2.45 unit which is close to the experimental value. The question is how can the diffusion coefficient be so close when density is not produced. Is this a mere coincidence? More likely a consequence of the water model itself. Keep in mind that SPC water is not real water, it does not reproduce all properties of water accurately. No water model does. Look into the literature for the expected density of SPC, but 980 does sound close to what is expected. Thinking that I used TIP4P water model with the same number but different force field ffG3a . I equilibrated the system to the same pressure and temperature with the same algorithms. After equilibration, the correspondng density was 991(+-) 15 kg/m3. Then I subjected it to the production run of 100ns. Now what I see is that the MSD curve is a hill, initially increasing, reaching maximum and again returning to the base. The diffusion coefficient is 0.7 unit for 100 ns of trajectory. What would have happened? Is this due to the increased density? Your precious knowledge on the subject matter would give me a sigh of relief. You must be careful interpreting your results. If you only have one molecule of your solute, then statistics will likely be very poor. You probably need either more solute molecules within a given system or many replicates of the same single-solute system to gather any meaningful data. The density of the system is a property dominated by the water model. I am also unsure of the validity of G96 parameters (but you haven't said which parameter set, ffG3a is not real) when combined with TIP4P. The Gromos force fields were parameterized with SPC; TIP4P is more often used with OPLS. I don't know exactly what effect that will have, but you should probably at least be using a robust combination, or demonstrate somehow that your application of the force field/water model is correct. -Justin Looking forward to hearing from you neal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] diffusion coefficient of oxygen
Hi, I would think this is one of very few examples where most of the force field is quite uncritical. Diffusion of a hydrophobic solute in water will mainly depend on the size of the solute and the diffusion coefficient of the water model itself. Of the common water models, SPC/E has the best diffusion coefficient and it combines well with the Gromos force fields, so use that. It is well known that the diffusion of SPC is twice what it should be. Berk Date: Wed, 10 Mar 2010 07:35:41 -0500 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] diffusion coefficient of oxygen Sunil Thapa wrote: Respected Experts I need your help In my study of diffusion of a oxygen molecule in 255 molecules of water, I previously used SPC water model with ffgmx force field with cutoff L-J and Coulomb interaction. I wanted to reproduce the experimental value 2.4 unit for diffusion coefficient of oxygen in water at 298 K and 1 atm. To equilibrate the system to the experimental water density of 997 I used Berendsen thermostat and the same barostat. The density of the system was 980(+-) 10 kg/m3 which is not the experimental value. After equilibration, I subjected the system to NVT ensemble md of 100 ns. I got the msd for oxygen molecule and analyzing first 4 ns (which was a st line part) of the plot, I got the diffusion coefficient of about 2.45 unit which is close to the experimental value. The question is how can the diffusion coefficient be so close when density is not produced. Is this a mere coincidence? More likely a consequence of the water model itself. Keep in mind that SPC water is not real water, it does not reproduce all properties of water accurately. No water model does. Look into the literature for the expected density of SPC, but 980 does sound close to what is expected. Thinking that I used TIP4P water model with the same number but different force field ffG3a . I equilibrated the system to the same pressure and temperature with the same algorithms. After equilibration, the correspondng density was 991(+-) 15 kg/m3. Then I subjected it to the production run of 100ns. Now what I see is that the MSD curve is a hill, initially increasing, reaching maximum and again returning to the base. The diffusion coefficient is 0.7 unit for 100 ns of trajectory. What would have happened? Is this due to the increased density? Your precious knowledge on the subject matter would give me a sigh of relief. You must be careful interpreting your results. If you only have one molecule of your solute, then statistics will likely be very poor. You probably need either more solute molecules within a given system or many replicates of the same single-solute system to gather any meaningful data. The density of the system is a property dominated by the water model. I am also unsure of the validity of G96 parameters (but you haven't said which parameter set, ffG3a is not real) when combined with TIP4P. The Gromos force fields were parameterized with SPC; TIP4P is more often used with OPLS. I don't know exactly what effect that will have, but you should probably at least be using a robust combination, or demonstrate somehow that your application of the force field/water model is correct. -Justin Looking forward to hearing from you neal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] diffusion coefficient of oxygen molecule
Respected experts I want to calculate the self diffusion cofficient of an oxygen molecule in water. The experimental value in the literature is found to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off Lennard Jones interaction between water and oxygen. I want to reproduce this value. In your experience, which model of water would give the closer value. I have seen that the self diffusion of SPC and TIP4P waters are 3.8 units and 3.2 units whereas the actual value is 2.4 unit. For oxygen the bonding potential has been taken to be harmonic. Any knowledge of related literature would be helpful because I could not find by googling. Your idea will really help me. Neal -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] diffusion coefficient of oxygen molecule
Sunil Thapa skrev: Respected experts I want to calculate the self diffusion cofficient of an oxygen molecule in water. The experimental value in the literature is found to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off Lennard Jones interaction between water and oxygen. I want to reproduce this value. In your experience, which model of water would give the closer value. I have seen that the self diffusion of SPC and TIP4P waters are 3.8 units and 3.2 units whereas the actual value is 2.4 unit. For oxygen the bonding potential has been taken to be harmonic. Any knowledge of related literature would be helpful because I could not find by googling. Your idea will really help me. Neal Hi, I do know that there are finite size effects that affects the diffusion coefficient, so you should make sure you use a big enough box. Furthermore, for water polarizability has an impact on the diffusion coefficient, so if you want to reproduce experimental values, consider using a polarizable model. -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] diffusion coefficient of oxygen molecule
Hi, If i remember correctly SPC/E water might be worth trying. There is plenty of research paper in this field. Try this paper http://pubs.acs.org/doi/abs/10.1021/jp003020w Also P,T coupling have effects on Diffusion Coeff. amit On Fri, Mar 5, 2010 at 1:29 AM, Sunil Thapa mephy...@yahoo.com wrote: Respected experts I want to calculate the self diffusion cofficient of an oxygen molecule in water. The experimental value in the literature is found to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off Lennard Jones interaction between water and oxygen. I want to reproduce this value. In your experience, which model of water would give the closer value. I have seen that the self diffusion of SPC and TIP4P waters are 3.8 units and 3.2 units whereas the actual value is 2.4 unit. For oxygen the bonding potential has been taken to be harmonic. Any knowledge of related literature would be helpful because I could not find by googling. Your idea will really help me. Neal -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] diffusion coefficient
Hi Everyone, I have been trying to calculate diffusion coefficient for water. I am trying to reproduce the numbers published in journal papers. I am using SPCE water model. I use the g_msd analysis tool. g_msd -f traj.trr -n index.ndx -s npt.tpr -b 2 -e 8 I use a box of volume 6x6x6 nm^3 which has 7161 water molecules. I equilibriate the system for a ns and then run for additional 10 ps for analysis. Here are some of the numbers that i get a. With Berendsen's T coupling and P coupling on i get 4.4941 (+/- 0.2992) 1e-5 cm^2/s b. With Berendsen's T coupling on and P coupling off I get 3.2469 (+/- 0.1076) 1e-5 cm^2/s c. With Berendsen's T coupling on and P coupling off for 1ns and then T,P coupling both off (for analysis part) i get 2.8085 (+/- 0.0310) 1e-5 cm^2/s . c is closest to the widely accepted experimental value of 2.3 1e-5 cm^2/s but its not quite right. Could someone explain to me why the values obtained in above 3 cases are widely different and may be give some tips about the right procedure to calculate diffusion (method and invoking the g_msd tool)? Thank you Amit -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] diffusion coefficient
Hi, you already have your solution at hand. On 10.02.2010, at 10:05, Amit Choubey wrote: Hi Everyone, I have been trying to calculate diffusion coefficient for water. I am trying to reproduce the numbers published in journal papers. I am using SPCE water model. I use the g_msd analysis tool. g_msd -f traj.trr -n index.ndx -s npt.tpr -b 2 -e 8 I use a box of volume 6x6x6 nm^3 which has 7161 water molecules. I equilibriate the system for a ns and then run for additional 10 ps for analysis. Here are some of the numbers that i get a. With Berendsen's T coupling and P coupling on i get 4.4941 (+/- 0.2992) 1e-5 cm^2/s b. With Berendsen's T coupling on and P coupling off I get 3.2469 (+/- 0.1076) 1e-5 cm^2/s c. With Berendsen's T coupling on and P coupling off for 1ns and then T,P coupling both off (for analysis part) i get 2.8085 (+/- 0.0310) 1e-5 cm^2/s . c is closest to the widely accepted experimental value of 2.3 1e-5 cm^2/s but its not quite right. You obtain a quite good estimation of the diffusion coefficient when not applying the Berendsen coupling scheme. The reason for this is that Berendsen coupling does not allow to generate a correct thermodynamic ensemble. Applying v-rescale or Nose-Hoover in combination with Parrinello-Rahman should yield more accurate results, because the take the way of sampling the phase space in an appropriate manner into account. Cheers, Flo Could someone explain to me why the values obtained in above 3 cases are widely different and may be give some tips about the right procedure to calculate diffusion (method and invoking the g_msd tool)? Thank you Amit -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert PGP.sig Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] diffusion coefficient
10 ps is too short of a trajectory, even for such a large system (for pure water it is considered large). i would guess that it is a typing-error and you ran for 10 ns? omer. On Wed, Feb 10, 2010 at 11:05, Amit Choubey kgp.a...@gmail.com wrote: I use a box of volume 6x6x6 nm^3 which has 7161 water molecules. I equilibriate the system for a ns and then run for additional 10 ps for analysis. Here are some of the numbers that i get -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Diffusion coefficient depenting on time interval
Hi users, I have simulated a box of NVT-water, more specifically the flexible urey-bradley-like TIPS-reparametrisation by Dang and Pettitt (1987). What I notice is that the diffusion coefficient increases when I calculate it from a longer snippet from my trajectory. If I use only 100 ps; starting at 100, 200 or 300 ps; the caculated coefficient is lower than if I use 400 ps (100-500 ps). Is this a known issue, inherent in the Einstein relation somehow? -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Diffusion coefficient depenting on time interval
Erik Marklund wrote: Hi users, I have simulated a box of NVT-water, more specifically the flexible urey-bradley-like TIPS-reparametrisation by Dang and Pettitt (1987). What I notice is that the diffusion coefficient increases when I calculate it from a longer snippet from my trajectory. If I use only 100 ps; starting at 100, 200 or 300 ps; the caculated coefficient is lower than if I use 400 ps (100-500 ps). Is this a known issue, inherent in the Einstein relation somehow? This is more a sampling issue I would think. Make your simulations even longer. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] diffusion coefficient with g_msd
On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote: Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate the diffusion coefficient of the molecules inside the membrane, and therefore I looked at g_msd. The manual (version 4.0) states on p. 250 (manual pages) that g_msd uses the Einstein relation. Reading Molecular Modelling: principles and applications 2.ed. by Andrew Leach it is explained that the for calculating the diffusion coefficient the mean-squared distances should not be limited by the edges of the periodic box. In other words, we require a set of positions that have not been translated back into the central simulation cell. This makes sense since I try to calculate the distance a molecule diffuse. I haven't been able to find any mention of how gromacs handle this either in the manual or on the wiki page. The search function on the old webpage directs me to the new webpage, which doesn't give any results for g_msd or diffusion coefficient or alike, so my apologies for asking a question I could have found the answer to I old emails. When I google I get some of the old emails on g_msd from the gromacs website, but I can only read some of them (the others direct me to an empty page in the new webpage). The first question is whether I can use my .xtc file made with this command from the original .trr file: trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc whole -s dmpclim32-1.tpr -o dmpclim32-all.xtc (for fitting and centring the DMPC group is used) I would guess I could not, but should I then do the command again creating a new .xtc file, but without using -center and -pbc whole? You are right. You can not use this trajectory. The fitting procedure will alter the diffusion of the system overall. If you had to do something it would be to use -pbc nojump to allow the molecules to freely diffuse. g_msd takes care of the periodicity of your system. So you do not have to fit or anything. My second question is why g_msd has the option -rmcomm to remove COM motion? How is g_msd created so that the diffusion coefficient can be calculated if COM motion is removed? The removal of the center of mass of the ENTIRE system is necessary before calculating the msd. This is generally done during the run using options in the mdp file. Which version you are using? I'd never seen the -rmcomm before? You can try to determine your msd with and without the option and see if it affects your result. This would depend on the removal or not of the COM motion in your simulation. XAvier. Thank you very much for your time, Sarah ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
SV: [gmx-users] diffusion coefficient with g_msd
Dear XAvier, Thank you very much for your answer. I have posted my .mdp file in the bottom of the email - as I haven't specified comm_mode or nstcomm, the default values should be used - this is also confirmed in the .log file: nstcomm = 1 comm_mode= Linear This should be fine, right? I have indeed removed the overall COM motion for each step of the simulation? Just to be sure: To convert the .trr file to an .xtc I could use this command: trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc whole -s dmpclim32-1.tpr -o dmpclim32-all.xtc I should not use -center (is that redundant when having nstcomm and comm_mode in the .mdp file?) or -fit rot+trans? Would your advice be to use -pbc nojump or just not -pbc at all? One last question: What is really the difference between -pbc nojumb and whole? I looked at g_msd -h for version 4.0.2, 4.0.3, and 4.0.4 (I'm using 4.0.4) and they all had the -rmcomm option, the manual version 3.3 doesn't mention it however. Thank you, Sarah #.mdp file# title= DMPC-LIM bilayer, 1 LIM and 128 lipids cpp = /lib/cpp integrator = md dt = 0.002 ; ps tinit= 0 init_step= 5000 nsteps = 7500 ;- ; Bond constraints define =; posres etc. constraints = all-bonds ; constrain all bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default ; X/V/F/E outputs nstxout = 5000 ; pos out --- 10 ps nstvout = 5000 ; vel out --- 10 ps nstfout = 0 ; force out --- no ;nstlog = 5000 ; energies to log (0.5 ps) nstenergy= 5000 ; energies to energy gile ; Neighbour list ns_type = grid ; neighlist type nstlist = 10; Freq. to update neighbour list rlist= 1.0 ; nm (cutoff for short-range NL) ; Coulomb interactions coulombtype = PME ; Particle Mesh Ewald rcoulomb = 1.0 ; nm (direct space sum cut-off) optimize_fft = yes ; optimal FFT plan for the grid ; van der Waals interactions vdwtype = Cut-off ; Van der Waals interactions rvdw = 1.0 ; nm (LJ cut-off) ; Temperature coupling Tcoupl = berendsen tc-grps = DMPC LIM_SOL tau_t = 0.1 0.1; ps ref_t = 310 310; K ; Energy monitoring energygrps = DMPC LIM_SOL ; Pressure coupling Pcoupl = berendsen Pcoupltype = semiisotropic; semi: (xy) and (z) separately tau_p = 1.0 1.0 ; ps compressibility = 4.5e-5 4.5e-5 ; 1/bar (water @ 1 atm, 300 K) ref_p = 1.0 1.0 ; bar # Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 09:34 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] diffusion coefficient with g_msd On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote: Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate the diffusion coefficient of the molecules inside the membrane, and therefore I looked at g_msd. The manual (version 4.0) states on p. 250 (manual pages) that g_msd uses the Einstein relation. Reading Molecular Modelling: principles and applications 2.ed. by Andrew Leach it is explained that the for calculating the diffusion coefficient the mean-squared distances should not be limited by the edges of the periodic box. In other words, we require a set of positions that have not been translated back into the central simulation cell. This makes sense since I try to calculate the distance a molecule diffuse. I haven't been able to find any mention of how gromacs handle this either in the manual or on the wiki page. The search function on the old webpage directs me to the new webpage, which doesn't give any results for g_msd or diffusion coefficient or alike, so my apologies for asking a question I could have found the answer to I old emails. When I google I get some of the old emails on g_msd from the gromacs website, but I can only read some of them (the others direct me to an empty page in the new webpage). The first question is whether I can use my .xtc file made with this command from the original .trr file: trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc whole -s dmpclim32-1.tpr -o dmpclim32-all.xtc (for fitting
Re: SV: [gmx-users] diffusion coefficient with g_msd
Sarah Witzke wrote: Dear XAvier, Thank you very much for your answer. I have posted my .mdp file in the bottom of the email - as I haven't specified comm_mode or nstcomm, the default values should be used - this is also confirmed in the .log file: nstcomm = 1 comm_mode= Linear For bilayer systems it is often recommended to removed the solvent and bilayer separately, they may move in opposite directions and also you remove the COM of the system the solvent and bilayer might move on relative to the other. This should be fine, right? I have indeed removed the overall COM motion for each step of the simulation? Just to be sure: To convert the .trr file to an .xtc I could use this command: trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc whole -s dmpclim32-1.tpr -o dmpclim32-all.xtc I should not use -center (is that redundant when having nstcomm and comm_mode in the .mdp file?) or -fit rot+trans? Would your advice be to use -pbc nojump or just not -pbc at all? One last question: What is really the difference between -pbc nojumb and whole? No, you just feed g_msd the trajectory trr the way it is. Or convert it in xtc if you like. You have to monitor the COM of the bilayer to check that the COM is indeed removed. For this you can do: 1) trjconv -f traj.trr -pbc nojump -o traj-nojump.xtc 2) g_traj -f traj-nojump.xtc -com -ox coord-COM.xvg -n index.ndx; in that step you choose the bilayer in your index and get the coordinates of the COM for which you can monitor the x, y and z values. I looked at g_msd -h for version 4.0.2, 4.0.3, and 4.0.4 (I'm using 4.0.4) and they all had the -rmcomm option, the manual version 3.3 doesn't mention it however. I was referring to the versions prior 4.0.X. It might be good to use it, it is definitely necessary to remove it. Thank you, Sarah #.mdp file# title= DMPC-LIM bilayer, 1 LIM and 128 lipids cpp = /lib/cpp integrator = md dt = 0.002 ; ps tinit= 0 init_step= 5000 nsteps = 7500 ;- ; Bond constraints define =; posres etc. constraints = all-bonds ; constrain all bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default ; X/V/F/E outputs nstxout = 5000 ; pos out --- 10 ps nstvout = 5000 ; vel out --- 10 ps nstfout = 0 ; force out --- no ;nstlog = 5000 ; energies to log (0.5 ps) nstenergy= 5000 ; energies to energy gile ; Neighbour list ns_type = grid ; neighlist type nstlist = 10; Freq. to update neighbour list rlist= 1.0 ; nm (cutoff for short-range NL) ; Coulomb interactions coulombtype = PME ; Particle Mesh Ewald rcoulomb = 1.0 ; nm (direct space sum cut-off) optimize_fft = yes ; optimal FFT plan for the grid ; van der Waals interactions vdwtype = Cut-off ; Van der Waals interactions rvdw = 1.0 ; nm (LJ cut-off) ; Temperature coupling Tcoupl = berendsen tc-grps = DMPC LIM_SOL tau_t = 0.1 0.1; ps ref_t = 310 310; K ; Energy monitoring energygrps = DMPC LIM_SOL ; Pressure coupling Pcoupl = berendsen Pcoupltype = semiisotropic; semi: (xy) and (z) separately tau_p = 1.0 1.0 ; ps compressibility = 4.5e-5 4.5e-5 ; 1/bar (water @ 1 atm, 300 K) ref_p = 1.0 1.0 ; bar # Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 09:34 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] diffusion coefficient with g_msd On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote: Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate the diffusion coefficient of the molecules inside the membrane, and therefore I looked at g_msd. The manual (version 4.0) states on p. 250 (manual pages) that g_msd uses the Einstein relation. Reading Molecular Modelling: principles and applications 2.ed. by Andrew Leach it is explained that the for calculating the diffusion coefficient the mean-squared distances should not be limited by the edges of the periodic box. In other words, we require a set of positions that have not been translated back into the central simulation cell. This makes
SV: SV: [gmx-users] diffusion coefficient with g_msd
Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 13:32 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] diffusion coefficient with g_msd Sarah Witzke wrote: Dear XAvier, Thank you very much for your answer. I have posted my .mdp file in the bottom of the email - as I haven't specified comm_mode or nstcomm, the default values should be used - this is also confirmed in the .log file: nstcomm = 1 comm_mode= Linear For bilayer systems it is often recommended to removed the solvent and bilayer separately, they may move in opposite directions and also you remove the COM of the system the solvent and bilayer might move on relative to the other. Thank you very much for telling me that. I'm sorry to ask, but how can you can you remove motion for the bilayer separately from the solvent? This should be fine, right? I have indeed removed the overall COM motion for each step of the simulation? Just to be sure: To convert the .trr file to an .xtc I could use this command: trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc whole -s dmpclim32-1.tpr -o dmpclim32-all.xtc I should not use -center (is that redundant when having nstcomm and comm_mode in the .mdp file?) or -fit rot+trans? Would your advice be to use -pbc nojump or just not -pbc at all? One last question: What is really the difference between -pbc nojumb and whole? No, you just feed g_msd the trajectory trr the way it is. Or convert it in xtc if you like. You have to monitor the COM of the bilayer to check that the COM is indeed removed. For this you can do: 1) trjconv -f traj.trr -pbc nojump -o traj-nojump.xtc 2) g_traj -f traj-nojump.xtc -com -ox coord-COM.xvg -n index.ndx; in that step you choose the bilayer in your index and get the coordinates of the COM for which you can monitor the x, y and z values. Oh, I'm sorry to have written my last email to fast, I meant to erase -center, -fit, and -pbc from the command :-( I'll try your suggestions with trjconv and g_traj. I looked at g_msd -h for version 4.0.2, 4.0.3, and 4.0.4 (I'm using 4.0.4) and they all had the -rmcomm option, the manual version 3.3 doesn't mention it however. I was referring to the versions prior 4.0.X. It might be good to use it, it is definitely necessary to remove it. Thank you, Sarah #.mdp file# title= DMPC-LIM bilayer, 1 LIM and 128 lipids cpp = /lib/cpp integrator = md dt = 0.002 ; ps tinit= 0 init_step= 5000 nsteps = 7500 ;- ; Bond constraints define =; posres etc. constraints = all-bonds ; constrain all bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default ; X/V/F/E outputs nstxout = 5000 ; pos out --- 10 ps nstvout = 5000 ; vel out --- 10 ps nstfout = 0 ; force out --- no ;nstlog = 5000 ; energies to log (0.5 ps) nstenergy= 5000 ; energies to energy gile ; Neighbour list ns_type = grid ; neighlist type nstlist = 10; Freq. to update neighbour list rlist= 1.0 ; nm (cutoff for short-range NL) ; Coulomb interactions coulombtype = PME ; Particle Mesh Ewald rcoulomb = 1.0 ; nm (direct space sum cut-off) optimize_fft = yes ; optimal FFT plan for the grid ; van der Waals interactions vdwtype = Cut-off ; Van der Waals interactions rvdw = 1.0 ; nm (LJ cut-off) ; Temperature coupling Tcoupl = berendsen tc-grps = DMPC LIM_SOL tau_t = 0.1 0.1; ps ref_t = 310 310; K ; Energy monitoring energygrps = DMPC LIM_SOL ; Pressure coupling Pcoupl = berendsen Pcoupltype = semiisotropic; semi: (xy) and (z) separately tau_p = 1.0 1.0 ; ps compressibility = 4.5e-5 4.5e-5 ; 1/bar (water @ 1 atm, 300 K) ref_p = 1.0 1.0 ; bar # Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 09:34 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] diffusion coefficient with g_msd On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote: Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate
Re: SV: SV: [gmx-users] diffusion coefficient with g_msd
Sarah Witzke wrote: Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 13:32 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] diffusion coefficient with g_msd Sarah Witzke wrote: Dear XAvier, Thank you very much for your answer. I have posted my .mdp file in the bottom of the email - as I haven't specified comm_mode or nstcomm, the default values should be used - this is also confirmed in the .log file: nstcomm = 1 comm_mode= Linear For bilayer systems it is often recommended to removed the solvent and bilayer separately, they may move in opposite directions and also you remove the COM of the system the solvent and bilayer might move on relative to the other. Thank you very much for telling me that. I'm sorry to ask, but how can you can you remove motion for the bilayer separately from the solvent? Use comm-grps and carefully-designed index groups. -Justin This should be fine, right? I have indeed removed the overall COM motion for each step of the simulation? Just to be sure: To convert the .trr file to an .xtc I could use this command: trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc whole -s dmpclim32-1.tpr -o dmpclim32-all.xtc I should not use -center (is that redundant when having nstcomm and comm_mode in the .mdp file?) or -fit rot+trans? Would your advice be to use -pbc nojump or just not -pbc at all? One last question: What is really the difference between -pbc nojumb and whole? No, you just feed g_msd the trajectory trr the way it is. Or convert it in xtc if you like. You have to monitor the COM of the bilayer to check that the COM is indeed removed. For this you can do: 1) trjconv -f traj.trr -pbc nojump -o traj-nojump.xtc 2) g_traj -f traj-nojump.xtc -com -ox coord-COM.xvg -n index.ndx; in that step you choose the bilayer in your index and get the coordinates of the COM for which you can monitor the x, y and z values. Oh, I'm sorry to have written my last email to fast, I meant to erase -center, -fit, and -pbc from the command :-( I'll try your suggestions with trjconv and g_traj. I looked at g_msd -h for version 4.0.2, 4.0.3, and 4.0.4 (I'm using 4.0.4) and they all had the -rmcomm option, the manual version 3.3 doesn't mention it however. I was referring to the versions prior 4.0.X. It might be good to use it, it is definitely necessary to remove it. Thank you, Sarah #.mdp file# title= DMPC-LIM bilayer, 1 LIM and 128 lipids cpp = /lib/cpp integrator = md dt = 0.002 ; ps tinit= 0 init_step= 5000 nsteps = 7500 ;- ; Bond constraints define =; posres etc. constraints = all-bonds ; constrain all bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default ; X/V/F/E outputs nstxout = 5000 ; pos out --- 10 ps nstvout = 5000 ; vel out --- 10 ps nstfout = 0 ; force out --- no ;nstlog = 5000 ; energies to log (0.5 ps) nstenergy= 5000 ; energies to energy gile ; Neighbour list ns_type = grid ; neighlist type nstlist = 10; Freq. to update neighbour list rlist= 1.0 ; nm (cutoff for short-range NL) ; Coulomb interactions coulombtype = PME ; Particle Mesh Ewald rcoulomb = 1.0 ; nm (direct space sum cut-off) optimize_fft = yes ; optimal FFT plan for the grid ; van der Waals interactions vdwtype = Cut-off ; Van der Waals interactions rvdw = 1.0 ; nm (LJ cut-off) ; Temperature coupling Tcoupl = berendsen tc-grps = DMPC LIM_SOL tau_t = 0.1 0.1; ps ref_t = 310 310; K ; Energy monitoring energygrps = DMPC LIM_SOL ; Pressure coupling Pcoupl = berendsen Pcoupltype = semiisotropic; semi: (xy) and (z) separately tau_p = 1.0 1.0 ; ps compressibility = 4.5e-5 4.5e-5 ; 1/bar (water @ 1 atm, 300 K) ref_p = 1.0 1.0 ; bar # Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 09:34 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] diffusion coefficient with g_msd On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote: Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate
[gmx-users] diffusion coefficient with g_msd
Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate the diffusion coefficient of the molecules inside the membrane, and therefore I looked at g_msd. The manual (version 4.0) states on p. 250 (manual pages) that g_msd uses the Einstein relation. Reading Molecular Modelling: principles and applications 2.ed. by Andrew Leach it is explained that the for calculating the diffusion coefficient the mean-squared distances should not be limited by the edges of the periodic box. In other words, we require a set of positions that have not been translated back into the central simulation cell. This makes sense since I try to calculate the distance a molecule diffuse. I haven't been able to find any mention of how gromacs handle this either in the manual or on the wiki page. The search function on the old webpage directs me to the new webpage, which doesn't give any results for g_msd or diffusion coefficient or alike, so my apologies for asking a question I could have found the answer to I old emails. When I google I get some of the old emails on g_msd from the gromacs website, but I can only read some of them (the others direct me to an empty page in the new webpage). The first question is whether I can use my .xtc file made with this command from the original .trr file: trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc whole -s dmpclim32-1.tpr -o dmpclim32-all.xtc (for fitting and centring the DMPC group is used) I would guess I could not, but should I then do the command again creating a new .xtc file, but without using -center and -pbc whole? My second question is why g_msd has the option -rmcomm to remove COM motion? How is g_msd created so that the diffusion coefficient can be calculated if COM motion is removed? Thank you very much for your time, Sarah ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
