[gmx-users] Diffusion Coefficient for hydration waters
Hi all, The diffusion coefficient can be calculated for the all the waters in the system, but how do calculate it for just the water molecules which are within 0.5 nm of the protein? Does anyone have any experience with this? I've tried to use gmx select to write an index file for the waters but as this is a dynamic selection, I would have to calculate each frame individually. Akash -- 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] Diffusion coefficient
On 9/17/17 6:05 PM, Dallas Warren wrote: http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html Don't know exactly how to do it myself, but there will be an option there where you can specify the z coordinate as a way to break it up into groups. And herein lies the challenge. The selections themselves will give index groups per frame, may vary in size, and the individual molecules themselves will likely occupy each slice discontinuously with respect to time. So a lot of effort would have to be made to make per-molecule sub-trajectories to compute a diffusion coefficient for a given time frame in which the molecule continuously satisfies the criterion, then calculated again over another period of time if the molecule moves out and comes back (otherwise one would get a spurious contribution to the MSD if a molecule seems to jump around). I suppose it can be done, but only very tediously in reassembling frames to make sub-trajectories, then looping over every molecule individually in doing so. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Diffusion coefficient
http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html Don't know exactly how to do it myself, but there will be an option there where you can specify the z coordinate as a way to break it up into groups. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On 17 September 2017 at 06:05, Sohaib. Mohammed wrote: > Any help! > > On Saturday, September 16, 2017, Sohaib. Mohammed < > sohaibmohamme...@gmail.com> wrote: > >> Hey Users, >> >> I want to calculate the diffusion coefficient using gmx msd. I want to >> divide the box into slices of 5 A parallel to z axis and calculate the >> diffusion coefficient for each slice. My question is how to make these >> slices, I've tried gmx trajconv but didn't work with me. I believe it's >> quite simple and provided by gromacs, but I am struggling with it. >> Appreciate any idea on how to make these slices. >> >> Thank you, >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Diffusion coefficient
Any help! On Saturday, September 16, 2017, Sohaib. Mohammed < sohaibmohamme...@gmail.com> wrote: > Hey Users, > > I want to calculate the diffusion coefficient using gmx msd. I want to > divide the box into slices of 5 A parallel to z axis and calculate the > diffusion coefficient for each slice. My question is how to make these > slices, I've tried gmx trajconv but didn't work with me. I believe it's > quite simple and provided by gromacs, but I am struggling with it. > Appreciate any idea on how to make these slices. > > Thank you, > -- 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] Diffusion coefficient
Hey Users, I want to calculate the diffusion coefficient using gmx msd. I want to divide the box into slices of 5 A parallel to z axis and calculate the diffusion coefficient for each slice. My question is how to make these slices, I've tried gmx trajconv but didn't work with me. I believe it's quite simple and provided by gromacs, but I am struggling with it. Appreciate any idea on how to make these slices. Thank you, -- 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] Diffusion coefficient
Hey Users, I want to calculate the diffusion coefficient using gmx msd. I want to divide the box into slices of 5 A parallel to z axis and calculate the diffusion coefficient for each slice. My question is how to make these slices, I've tried gmx trajconv but didn't work with me. I believe it's quite simple and provided by gromacs, but I am struggling with it. Appreciate any idea on how to make these slices. Thank you, Sohaib -- 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] Diffusion coefficient water
The following paper may also be interesting. "System-size corrections for self-diffusion coefficients calculated from molecular dynamics simulations: The case of CO2, n-alkanes, and poly(ethylene glycol) dimethyl ether" J. Chem. Phys. 145, 074109 (2016); http://dx.doi.org/10.1063/1.4960776 2016-08-18 8:35 GMT-05:00 Michael Shirts : > See the following paper > (http://pubs.acs.org/doi/abs/10.1021/ct400109a) for some examples of > diffusion calculations in GROMACS. > > The finite size correction for diffusion coefficients is something > different than the long range energy corrections. A discussion of this > (I can't vouch for all the details, I just googled) is here: > http://pubs.acs.org/doi/abs/10.1021/jp0756247 > > -- 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] Diffusion coefficient water
See the following paper (http://pubs.acs.org/doi/abs/10.1021/ct400109a) for some examples of diffusion calculations in GROMACS. The finite size correction for diffusion coefficients is something different than the long range energy corrections. A discussion of this (I can't vouch for all the details, I just googled) is here: http://pubs.acs.org/doi/abs/10.1021/jp0756247 On Thu, Aug 18, 2016 at 6:37 AM, Mark Abraham wrote: > Hi, > > I would also consider using a pressure-coupling algorithm that isn't known > to create the wrong velocity distribution. > > Mark > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Diffusion coefficient water
Hi, I would also consider using a pressure-coupling algorithm that isn't known to create the wrong velocity distribution. Mark -- 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] Diffusion coefficient water
On 8/18/16 6:48 AM, Diez Fernandez, Amanda wrote: Thanks Justin and Nikhil, 1) So in principle is it expected that results will be different and I should take my final value to be the average of, say, 10 simulations? Yes, averaging over multiple, independent simulations is the correct approach. 2)If so, the average over my simulations is not similar to the published average. They also use a unit cell of 216 molecules (I use 221 molecules). They have "long-range corrections for both the energy and pressure². Is this equivalent to DispCorr= EnerPres ? What other corrections should I do? DispCorr = EnerPres is correct. If you're having trouble reproducing a published result, you should ask the authors of the study for their advice. -Justin Thanks, Amanda On 17/08/2016, 19:28, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se" wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. Re: Diffusion coefficient water (Nikhil Maroli) 2. Re: Diffusion coefficient water (Justin Lemkul) 3. is there martini CG parameters for K+ ion? (li he) 4. Re: Diffusion coefficient water (li he) 5. Fwd: is there martini CG parameters for K+ ion? (li he) 6. Re: Diffusion coefficient water (li he) -- Message: 1 Date: Wed, 17 Aug 2016 21:49:45 +0530 From: Nikhil Maroli To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Diffusion coefficient water Message-ID: Content-Type: text/plain; charset=UTF-8 I don't think we can reproduce the exact results in MD .The overall behaviour of the system will be same .so it's obvious -- Message: 2 Date: Wed, 17 Aug 2016 13:11:02 -0400 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Diffusion coefficient water Message-ID: <8eb7b1ee-041c-906d-f7a1-7e6d683c4...@vt.edu> Content-Type: text/plain; charset=windows-1252; format=flowed On 8/17/16 11:28 AM, Diez Fernandez, Amanda wrote: Dear Gromacs users, I was trying to reproduce the published values for the diffusion coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using it in some of my simulations and I am failing to do so. More worryingly I get different results for different identical runs. I am using a 2nm side cubic cell containing 221 water molecules and a time step of 0.5fs (larger timestep results in a warning since I am not applying any constraints). I ran 6 identical simulations (only difference is the random initial velocities) and I got these different values and error magnitudes. The trajectories are 10ns long. I discarded the first 2ns for the msd calculation. Nth Simulation Diffusion Coefficient (x 10^-9 m^2/s) 1 2.95 +/- 0.071 2 2.71 +/- 0.158 3 2.52 +/- 0.007 4 2.96 +/- 0.26 5 2.62 +/- 0.07 6 2.71 +/- 0.158 Is it normal that I get different results like this? (Despite averaging over more than 7ns and 221 molecules?). Diffusion constants are subject to finite-size effects. Have you corrected for this phenomenon? And perhaps more importantly, did the original authors of the water model correct their values? I find that often times people don't, or otherwise don't say if the correction has been applied. 2 nm is a very small box, so the PBC correction will be quite substantial. -Justin Many thanks in advance. Below are the detailed parameters. Amanda Detailed parameters: nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-6 vdw-type= cut-off rvdw= 0.9 pbc = xyz tcoupl = nose-hoover tc_grps = SYSTEM tau_t = 0.4 ref_t = 298 nsttcouple =-1 nh-chain-length = 1 pcoupl = Berendsen pcoupltype
Re: [gmx-users] Diffusion coefficient water
Thanks Justin and Nikhil, 1) So in principle is it expected that results will be different and I should take my final value to be the average of, say, 10 simulations? 2)If so, the average over my simulations is not similar to the published average. They also use a unit cell of 216 molecules (I use 221 molecules). They have "long-range corrections for both the energy and pressure². Is this equivalent to DispCorr= EnerPres ? What other corrections should I do? Thanks, Amanda On 17/08/2016, 19:28, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se" wrote: >Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > >To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > >You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of gromacs.org_gmx-users digest..." > > >Today's Topics: > > 1. Re: Diffusion coefficient water (Nikhil Maroli) > 2. Re: Diffusion coefficient water (Justin Lemkul) > 3. is there martini CG parameters for K+ ion? (li he) > 4. Re: Diffusion coefficient water (li he) > 5. Fwd: is there martini CG parameters for K+ ion? (li he) > 6. Re: Diffusion coefficient water (li he) > > >-- > >Message: 1 >Date: Wed, 17 Aug 2016 21:49:45 +0530 >From: Nikhil Maroli >To: gromacs.org_gmx-users@maillist.sys.kth.se >Subject: Re: [gmx-users] Diffusion coefficient water >Message-ID: > >Content-Type: text/plain; charset=UTF-8 > >I don't think we can reproduce the exact results in MD .The overall >behaviour of the system will be same .so it's obvious > > >------ > >Message: 2 >Date: Wed, 17 Aug 2016 13:11:02 -0400 >From: Justin Lemkul >To: gmx-us...@gromacs.org >Subject: Re: [gmx-users] Diffusion coefficient water >Message-ID: <8eb7b1ee-041c-906d-f7a1-7e6d683c4...@vt.edu> >Content-Type: text/plain; charset=windows-1252; format=flowed > > > >On 8/17/16 11:28 AM, Diez Fernandez, Amanda wrote: >> Dear Gromacs users, >> >> I was trying to reproduce the published values for the diffusion >>coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using it >>in some of my simulations and I am failing to do so. >> More worryingly I get different results for different identical runs. >> I am using a 2nm side cubic cell containing 221 water molecules and a >>time step of 0.5fs (larger timestep results in a warning since I am not >>applying any constraints). >> I ran 6 identical simulations (only difference is the random initial >>velocities) and I got these different values and error magnitudes. >> The trajectories are 10ns long. I discarded the first 2ns for the msd >>calculation. >> >> Nth Simulation Diffusion Coefficient (x 10^-9 m^2/s) >> >> 1 2.95 +/- 0.071 >> 2 2.71 +/- 0.158 >> 3 2.52 +/- 0.007 >> 4 2.96 +/- 0.26 >> 5 2.62 +/- 0.07 >> 6 2.71 +/- 0.158 >> >> Is it normal that I get different results like this? (Despite >>averaging over more than 7ns and 221 molecules?). >> > >Diffusion constants are subject to finite-size effects. Have you >corrected for >this phenomenon? And perhaps more importantly, did the original authors >of the >water model correct their values? I find that often times people don't, >or >otherwise don't say if the correction has been applied. 2 nm is a very >small >box, so the PBC correction will be quite substantial. > >-Justin > >> Many thanks in advance. Below are the detailed parameters. >> >> Amanda >> >> Detailed parameters: >> >> nstlist = 10 >> >> ns_type = grid >> >> rlist = 0.9 >> >> coulombtype = PME >> >> rcoulomb= 0.9 >> >> fourierspacing = 0.12 >> >> pme_order = 4 >>
Re: [gmx-users] Diffusion coefficient water
4. you could even try NVT ensemble 2016-08-18 2:25 GMT+08:00 li he : > I think you could try following things to see if you could get 'better' > results > 1. use time step of 0.2 or even 0.1 fs > 2. try different tau-t and tau-p, e.g. use larger tau-t > 3. try different p-coupling methods > > 2016-08-17 23:28 GMT+08:00 Diez Fernandez, Amanda < > amanda.die...@imperial.ac.uk>: > >> Dear Gromacs users, >> >> I was trying to reproduce the published values for the diffusion >> coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using it in >> some of my simulations and I am failing to do so. >> More worryingly I get different results for different identical runs. >> I am using a 2nm side cubic cell containing 221 water molecules and a >> time step of 0.5fs (larger timestep results in a warning since I am not >> applying any constraints). >> I ran 6 identical simulations (only difference is the random initial >> velocities) and I got these different values and error magnitudes. >> The trajectories are 10ns long. I discarded the first 2ns for the msd >> calculation. >> >> Nth Simulation Diffusion Coefficient (x 10^-9 m^2/s) >> >> 1 2.95 +/- 0.071 >> 2 2.71 +/- 0.158 >> 3 2.52 +/- 0.007 >> 4 2.96 +/- 0.26 >> 5 2.62 +/- 0.07 >> 6 2.71 +/- 0.158 >> >> Is it normal that I get different results like this? (Despite averaging >> over more than 7ns and 221 molecules?). >> >> Many thanks in advance. Below are the detailed parameters. >> >> Amanda >> >> Detailed parameters: >> >> nstlist = 10 >> >> ns_type = grid >> >> rlist = 0.9 >> >> coulombtype = PME >> >> rcoulomb= 0.9 >> >> fourierspacing = 0.12 >> >> pme_order = 4 >> >> ewald_rtol = 1e-6 >> >> vdw-type= cut-off >> >> rvdw= 0.9 >> >> pbc = xyz >> >> tcoupl = nose-hoover >> >> tc_grps = SYSTEM >> >> tau_t = 0.4 >> >> ref_t = 298 >> >> nsttcouple =-1 >> >> nh-chain-length = 1 >> >> pcoupl = Berendsen >> >> pcoupltype = isotropic >> >> tau_p = 10.0 >> >> compressibility = 4.5e-5 >> >> ref_p = 1.01325 >> >> refcoord-scaling= all >> >> DispCorr= EnerPres >> >> gen_vel = yes >> >> gen_temp= 293 >> >> gen_seed= -1 >> >> constraints = none >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Diffusion coefficient water
I think you could try following things to see if you could get 'better' results 1. use time step of 0.2 or even 0.1 fs 2. try different tau-t and tau-p, e.g. use larger tau-t 3. try different p-coupling methods 2016-08-17 23:28 GMT+08:00 Diez Fernandez, Amanda < amanda.die...@imperial.ac.uk>: > Dear Gromacs users, > > I was trying to reproduce the published values for the diffusion > coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using it in > some of my simulations and I am failing to do so. > More worryingly I get different results for different identical runs. > I am using a 2nm side cubic cell containing 221 water molecules and a time > step of 0.5fs (larger timestep results in a warning since I am not applying > any constraints). > I ran 6 identical simulations (only difference is the random initial > velocities) and I got these different values and error magnitudes. > The trajectories are 10ns long. I discarded the first 2ns for the msd > calculation. > > Nth Simulation Diffusion Coefficient (x 10^-9 m^2/s) > > 1 2.95 +/- 0.071 > 2 2.71 +/- 0.158 > 3 2.52 +/- 0.007 > 4 2.96 +/- 0.26 > 5 2.62 +/- 0.07 > 6 2.71 +/- 0.158 > > Is it normal that I get different results like this? (Despite averaging > over more than 7ns and 221 molecules?). > > Many thanks in advance. Below are the detailed parameters. > > Amanda > > Detailed parameters: > > nstlist = 10 > > ns_type = grid > > rlist = 0.9 > > coulombtype = PME > > rcoulomb= 0.9 > > fourierspacing = 0.12 > > pme_order = 4 > > ewald_rtol = 1e-6 > > vdw-type= cut-off > > rvdw= 0.9 > > pbc = xyz > > tcoupl = nose-hoover > > tc_grps = SYSTEM > > tau_t = 0.4 > > ref_t = 298 > > nsttcouple =-1 > > nh-chain-length = 1 > > pcoupl = Berendsen > > pcoupltype = isotropic > > tau_p = 10.0 > > compressibility = 4.5e-5 > > ref_p = 1.01325 > > refcoord-scaling= all > > DispCorr= EnerPres > > gen_vel = yes > > gen_temp= 293 > > gen_seed= -1 > > constraints = none > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Diffusion coefficient water
On 8/17/16 11:28 AM, Diez Fernandez, Amanda wrote: Dear Gromacs users, I was trying to reproduce the published values for the diffusion coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using it in some of my simulations and I am failing to do so. More worryingly I get different results for different identical runs. I am using a 2nm side cubic cell containing 221 water molecules and a time step of 0.5fs (larger timestep results in a warning since I am not applying any constraints). I ran 6 identical simulations (only difference is the random initial velocities) and I got these different values and error magnitudes. The trajectories are 10ns long. I discarded the first 2ns for the msd calculation. Nth Simulation Diffusion Coefficient (x 10^-9 m^2/s) 1 2.95 +/- 0.071 2 2.71 +/- 0.158 3 2.52 +/- 0.007 4 2.96 +/- 0.26 5 2.62 +/- 0.07 6 2.71 +/- 0.158 Is it normal that I get different results like this? (Despite averaging over more than 7ns and 221 molecules?). Diffusion constants are subject to finite-size effects. Have you corrected for this phenomenon? And perhaps more importantly, did the original authors of the water model correct their values? I find that often times people don't, or otherwise don't say if the correction has been applied. 2 nm is a very small box, so the PBC correction will be quite substantial. -Justin Many thanks in advance. Below are the detailed parameters. Amanda Detailed parameters: nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-6 vdw-type= cut-off rvdw= 0.9 pbc = xyz tcoupl = nose-hoover tc_grps = SYSTEM tau_t = 0.4 ref_t = 298 nsttcouple =-1 nh-chain-length = 1 pcoupl = Berendsen pcoupltype = isotropic tau_p = 10.0 compressibility = 4.5e-5 ref_p = 1.01325 refcoord-scaling= all DispCorr= EnerPres gen_vel = yes gen_temp= 293 gen_seed= -1 constraints = none -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Diffusion coefficient water
I don't think we can reproduce the exact results in MD .The overall behaviour of the system will be same .so it's obvious -- 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] Diffusion coefficient water
Dear Gromacs users, I was trying to reproduce the published values for the diffusion coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using it in some of my simulations and I am failing to do so. More worryingly I get different results for different identical runs. I am using a 2nm side cubic cell containing 221 water molecules and a time step of 0.5fs (larger timestep results in a warning since I am not applying any constraints). I ran 6 identical simulations (only difference is the random initial velocities) and I got these different values and error magnitudes. The trajectories are 10ns long. I discarded the first 2ns for the msd calculation. Nth Simulation Diffusion Coefficient (x 10^-9 m^2/s) 1 2.95 +/- 0.071 2 2.71 +/- 0.158 3 2.52 +/- 0.007 4 2.96 +/- 0.26 5 2.62 +/- 0.07 6 2.71 +/- 0.158 Is it normal that I get different results like this? (Despite averaging over more than 7ns and 221 molecules?). Many thanks in advance. Below are the detailed parameters. Amanda Detailed parameters: nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-6 vdw-type= cut-off rvdw= 0.9 pbc = xyz tcoupl = nose-hoover tc_grps = SYSTEM tau_t = 0.4 ref_t = 298 nsttcouple =-1 nh-chain-length = 1 pcoupl = Berendsen pcoupltype = isotropic tau_p = 10.0 compressibility = 4.5e-5 ref_p = 1.01325 refcoord-scaling= all DispCorr= EnerPres gen_vel = yes gen_temp= 293 gen_seed= -1 constraints = none -- 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] Diffusion coefficient of metal complex
On 7/23/14, 7:13 AM, Meena Singh wrote: Dear GROMACS users, I'm working on the diffusivity of metal ion with its ligand in organic phase. I want to calculate the diffusion coefficient of metal-ligand complex as a group, but when I run g_msd command the option are there for only individual molecules diffusivity calculation. Can I calculate the diffusion coefficient of specific complex from the box which contains metal ions and ligand molecules. Does anyone have a suggestion to help me with this problem? Create an index group for whatever subset of atoms you like and use it for the calculation. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Diffusion coefficient of metal complex
Dear GROMACS users, I'm working on the diffusivity of metal ion with its ligand in organic phase. I want to calculate the diffusion coefficient of metal-ligand complex as a group, but when I run g_msd command the option are there for only individual molecules diffusivity calculation. Can I calculate the diffusion coefficient of specific complex from the box which contains metal ions and ligand molecules. Does anyone have a suggestion to help me with this problem? -- *Regards,* *Meena Singh* *Ph. D. Research Scholar* *Chem Engg Dept,* *Institute of Chemical Technology, Mumbai * -- 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.