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" <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 <scinik...@gmail.com> >To: gromacs.org_gmx-users@maillist.sys.kth.se >Subject: Re: [gmx-users] Diffusion coefficient water >Message-ID: > <CAMEzy6QX0q5dF94ykgOckdtvZxZwpwpsY6-=bu1w2k160ff...@mail.gmail.com> >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 <jalem...@vt.edu> >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 = 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 > >================================================== > > >------------------------------ > >Message: 3 >Date: Thu, 18 Aug 2016 02:17:28 +0800 >From: li he <parachuternewy...@gmail.com> >To: gromacs.org_gmx-users@maillist.sys.kth.se >Subject: [gmx-users] is there martini CG parameters for K+ ion? >Message-ID: > <cagrcqu7aye6jsd_1mbyykodqom-htfukakk7xn5nnjv_muc...@mail.gmail.com> >Content-Type: text/plain; charset=UTF-8 > >Dear gmxers, >I am not sure if I'd better post my question here, but the martini forum >http://www.cgmartini.nl/index.php/forum does not allow me register and >post my >question there. >I am trying to simulate some KCl solution, but only find martini CG Na+ >parameters >at http://cgmartini.nl/images/parameters/ITP/martini_v2.0_ions.itp >I am wondering where I can find martini parameters for K+ ion, or can I >just use martini >Na+ parameters for K+? >If there is a martini parameter of K+, I could image it should be Qd bead >with +1 charge, exactly the same as Na+ parameters at the above link. Yes, >it is upsetting to use the same parameter for Na+ and K+, but we have to >admit the current martini force field is not very fine tuned, thus have to >just use Na+ martini parameters at the above link for K+ if we want to >simulate CG KCl or martini KCl anyway? Can this way be justified if the >simulation results agree with the results of other studies, either >experiments or simulations? >Thanks a lot for your kind help, and any suggestion or comment is very >welcome. >Yours >he li > > >------------------------------ > >Message: 4 >Date: Thu, 18 Aug 2016 02:25:09 +0800 >From: li he <parachuternewy...@gmail.com> >To: gmx-us...@gromacs.org >Subject: Re: [gmx-users] Diffusion coefficient water >Message-ID: > <cagrcqu74vaoabsofzjr67pnifqc3bdjes7xo0umf96ze3kv...@mail.gmail.com> >Content-Type: text/plain; charset=UTF-8 > >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. >> > > >------------------------------ > >Message: 5 >Date: Thu, 18 Aug 2016 02:26:37 +0800 >From: li he <parachuternewy...@gmail.com> >To: gmx-us...@gromacs.org >Subject: [gmx-users] Fwd: is there martini CG parameters for K+ ion? >Message-ID: > <cagrcqu5wylvrnkibcfhvyomtqomnomxwzef-w1hcgojepnz...@mail.gmail.com> >Content-Type: text/plain; charset=UTF-8 > >Dear gmxers, >I am not sure if I'd better post my question here, but the martini forum >http://www.cgmartini.nl/index.php/forum does not allow me register and >post my >question there. >I am trying to simulate some KCl solution, but only find martini CG Na+ >parameters >at http://cgmartini.nl/images/parameters/ITP/martini_v2.0_ions.itp >I am wondering where I can find martini parameters for K+ ion, or can I >just use martini >Na+ parameters for K+? >If there is a martini parameter of K+, I could image it should be Qd bead >with +1 charge, exactly the same as Na+ parameters at the above link. Yes, >it is upsetting to use the same parameter for Na+ and K+, but we have to >admit the current martini force field is not very fine tuned, thus have to >just use Na+ martini parameters at the above link for K+ if we want to >simulate CG KCl or martini KCl anyway? Can this way be justified if the >simulation results agree with the results of other studies, either >experiments or simulations? >Thanks a lot for your kind help, and any suggestion or comment is very >welcome. >Yours >he li > > >------------------------------ > >Message: 6 >Date: Thu, 18 Aug 2016 02:27:58 +0800 >From: li he <parachuternewy...@gmail.com> >To: gmx-us...@gromacs.org >Subject: Re: [gmx-users] Diffusion coefficient water >Message-ID: > <cagrcqu577udfgywjmaxrobajsuln3d6wo_uhiy83ti1zt1m...@mail.gmail.com> >Content-Type: text/plain; charset=UTF-8 > >4. you could even try NVT ensemble > >2016-08-18 2:25 GMT+08:00 li he <parachuternewy...@gmail.com>: > >> 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. > >End of gromacs.org_gmx-users Digest, Vol 148, Issue 68 >****************************************************** -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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