On Mon, Jan 17, 2011 at 8:29 AM, <[email protected]> wrote:
> Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: Non integral charges (Erik Marklund) > 2. Re: Non integral charges (Justin A. Lemkul) > 3. Re: Viscosity calculations (Justin A. Lemkul) > 4. Re: Non integral charges (Kavyashree M) > 5. Secondary structure loss in implicit solvent simulations > (K. Singhal) > 6. Re: Non integral charges (Vitaly Chaban) > 7. Re: Re: Non integral charges (Justin A. Lemkul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 17 Jan 2011 13:06:19 +0100 > From: Erik Marklund <[email protected]> > Subject: Re: [gmx-users] Non integral charges > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > It's pretty close to -1. The difference stems from floating point > conversion errors. There's nothing to worry about. > > Erik > > Kavyashree M skrev 2011-01-17 13.02: > > Dear gromacs users, > > > > while using grompp I got a message : > > > > " System has non-zero total charge: -9.999998e-01" > > > > This is non integral charges. What should I add using genion? > > +1 charge? Why am I getting such non integral charges? > > I also checked for any breakage in the chain and found no such > > ends. > > > > Kindly suggest > > > > With Regards > > MKS > > > > > > > -- > ----------------------------------------------- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > [email protected] http://folding.bmc.uu.se/ > > > > ------------------------------ > > Message: 2 > Date: Mon, 17 Jan 2011 07:07:51 -0500 > From: "Justin A. Lemkul" <[email protected]> > Subject: Re: [gmx-users] Non integral charges > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Kavyashree M wrote: > > Dear gromacs users, > > > > while using grompp I got a message : > > > > " System has non-zero total charge: -9.999998e-01" > > > > This is non integral charges. What should I add using genion? > > +1 charge? Why am I getting such non integral charges? > > Please see FAQ #30. > > http://www.gromacs.org/Documentation/FAQs > > -Justin > > > I also checked for any breakage in the chain and found no such > > ends. > > > > Kindly suggest > > > > With Regards > > MKS > > > > > > -- > ======================================== > > 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 > > ======================================== > > > ------------------------------ > > Message: 3 > Date: Mon, 17 Jan 2011 07:11:29 -0500 > From: "Justin A. Lemkul" <[email protected]> > Subject: Re: [gmx-users] Viscosity calculations > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Xiaohu Li wrote: > > Hi, > > I'm trying to calculate viscosities of a few ionic liquid and has > > roughly read about Hess's paper JCP 116 209, 2002. > > Follows are the questions that I have > > (1) For the method which uses the fluctuations of the pressure tensor > > using Green-Kubo relation. I used g_energy -f *.edr -s *.tpr -vis option > > and has obtained > > a few files such as evisco.xvg, eviscoi.xvg and visco.xvg > > The evisco.xvg seems like the one I'm interested, since it has the title > as > > @ title "Shear viscosity using Einstein relation" > > and the unit seems also correct. This file has 5 columns, if I > > understand it correctly(by extrapolating from Hess's paper), the second > > to fourth columns are the results from the off-diagonal elements of the > > pressure > > tensor and the fifth one being the average. Hess's paper seems to be > > this one(Figure 5). However, the results are way to low for the ionic > > liquid, since I'm getting 1e-7 kg/m.s and way too low for a ionic liquid. > > the eviscoi.xvg file seems to be some kind of integral of evisco.xvg > > which I'm not quite getting what it is. > > visco.xvg contains the shear viscosity and bulk viscosity, which again > > seems to be the one I'm looking for. However, the shear viscosity I'm > > looking is(the region which roughly is constant) about 3~5 times higher > > than the experiment. The simulation is 12ns long. Of course, this could > > mean (1) the force field is bad or (2) the Green-kudo converges too > > slowly as Hess pointed out. > > Either of these are possible. Have you tried (1) different parameters or > (2) > longer simulations? If the model does not reproduce the experiment, it is > not a > very good model... > What about those files evisco.xvg, eviscoi.xvg and visco.xvg? which one could be the correct file to look at? I'm using OPLS-AA force field, the density and enthalpy of evaporation are both reasonably reproduced. However, kinetic studies using OPLS-AA on ionic liquid seems scarce(or I know little enough to not aware of what has been done). > > > Since it is not getting any useful result, I turned to non-equilibrium > > MD by applying a shear external force, which is in (2) > > (2) I tried both NVT and NPT simulations which uses berendsen coupling > > bath. and set up the cos_acceleration = 0.1 nm/ps^2. > > However, I tried to use g_energy -f *edr -s *tpr and by selecting > > the 1/Viscosity or 2CosZ*Vel-X option, the output are giving me zero > > data points on all times. > > > > This could be related to a bug that was fixed just a few days ago. Try > pulling > the latest stable release from git and trying again. > That sounds like a solution, can you provide a link? > > -Justin > > > I tried really hard on searching results on the user list of gromacs > > but it seems that there are quite a lot questions on this but not a > > single satisfactory answer has been given, the most popular answer > > people gave is refer to Hess's paper, but even though Hess was giving a > > good theoretical background on this paper, practically on how to set up > > MD jobs is not given. > > So I would appreciate anyone's hint. > > > > Cheers, > > > > Xiaohu > > > > -- > ======================================== > > 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 > > ======================================== > > > ------------------------------ > > Message: 4 > Date: Mon, 17 Jan 2011 17:41:51 +0530 > From: Kavyashree M <[email protected]> > Subject: Re: [gmx-users] Non integral charges > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > Thank you Sir! > > With Regards > MKS > > On Mon, Jan 17, 2011 at 5:37 PM, Justin A. Lemkul <[email protected]> wrote: > > > > > > > Kavyashree M wrote: > > > >> Dear gromacs users, > >> > >> while using grompp I got a message : > >> > >> " System has non-zero total charge: -9.999998e-01" > >> > >> This is non integral charges. What should I add using genion? > >> +1 charge? Why am I getting such non integral charges? > >> > > > > Please see FAQ #30. > > > > http://www.gromacs.org/Documentation/FAQs > > > > -Justin > > > > > > I also checked for any breakage in the chain and found no such > >> ends. > >> > >> Kindly suggest > >> > >> With Regards > >> MKS > >> > >> > >> > > -- > > ======================================== > > > > 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 list [email protected] > > 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 [email protected]. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110117/3b71fe67/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Mon, 17 Jan 2011 14:45:37 +0100 > From: "K. Singhal" <[email protected]> > Subject: [gmx-users] Secondary structure loss in implicit solvent > simulations > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=us-ascii > > Hi > > I have a question regarding the implicit solvent implementation in GROMACS > 4.5.1 (with GPU acceleration). I have been trying to simulate molecules with > varying size (PYP with 125 AAs, BBA5 with ~20 AAs, and and Trigger Factor > with 432 AAs), but can't seem to be able to maintain the secondary structure > in any of them. Can any one suggest a particular set of parameters than need > to be taken care of or used with certain fixed values for better results? > > While I have used a varied range of values for almost all parameters, here > is the list of parameters recently and unsuccessfully used: > integrator = sd > nsteps = 10000000 > init_step = 0 > ns_type = Grid > nstlist = 10 > ndelta = 2 > nstcomm = 10 > comm_mode = Linear > delta_t = 0.002 > pme_order = 4 > ewald_rtol = 1e-05 > ewald_geometry = 0 > epsilon_surface = 0 > optimize_fft = FALSE > ePBC = xyz > bPeriodicMols = FALSE > bContinuation = FALSE > bShakeSOR = FALSE > etc = No > nsttcouple = -1 > epc = No > epctype = Isotropic > nstpcouple = -1 > tau_p = 1 > andersen_seed = 815131 > rlist = 1.1 > rlistlong = 2.5 > rtpi = 0.05 > coulombtype = Cut-off > rcoulomb_switch = 0 > rcoulomb = 2.5 > vdwtype = Cut-off > rvdw_switch = 0 > rvdw = 2.5 > epsilon_r = 1 > epsilon_rf = 1 > implicit_solvent = GBSA > gb_algorithm = OBC > gb_epsilon_solvent = 80 > nstgbradii = 1 > rgbradii = 1.1 > gb_saltconc = 0.02 > gb_obc_alpha = 1 > gb_obc_beta = 0.8 > gb_obc_gamma = 4.85 > gb_dielectric_offset = 0.009 > sa_algorithm = Still > sa_surface_tension = 2.092 > shake_tol = 7.5e-06 > bd_fric = 0.5 > ld_seed = 2010 > > Thanks and Regards > Kush > > > > -- > Kushagra Singhal > Promovendus, Computational Chemistry > Universiteit van Amsterdam > > > > ------------------------------ > > Message: 6 > Date: Mon, 17 Jan 2011 09:25:53 -0500 > From: Vitaly Chaban <[email protected]> > Subject: [gmx-users] Re: Non integral charges > To: [email protected] > Message-ID: > > <[email protected]<aanlktimflitxcgehotucxm1erau57c9eaemciyik4c%[email protected]> > > > Content-Type: text/plain; charset=ISO-8859-1 > > > while using grompp I got a message : > > > > " System has non-zero total charge: -9.999998e-01" > > > > This is non integral charges. What should I add using genion? > > +1 charge? Why am I getting such non integral charges? > > I also checked for any breakage in the chain and found no such > > ends. > > > > Kindly suggest > > > > With Regards > > MKS > > Dear MKS: > > You should check the topology file(s) personally since it(they) > presumably not healthy. > > -- > ========================= > Dr. Vitaly V. Chaban, Ph.D. > Department of Chemistry > University of Rochester > Rochester, New York 14627-0216 > The United States of America > ========================= > > > ------------------------------ > > Message: 7 > Date: Mon, 17 Jan 2011 09:28:44 -0500 > From: "Justin A. Lemkul" <[email protected]> > Subject: Re: [gmx-users] Re: Non integral charges > To: [email protected], Discussion list for GROMACS users > <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Vitaly Chaban wrote: > >> while using grompp I got a message : > >> > >> " System has non-zero total charge: -9.999998e-01" > >> > >> This is non integral charges. What should I add using genion? > >> +1 charge? Why am I getting such non integral charges? > >> I also checked for any breakage in the chain and found no such > >> ends. > >> > >> Kindly suggest > >> > >> With Regards > >> MKS > > > > Dear MKS: > > > > You should check the topology file(s) personally since it(they) > > presumably not healthy. > > > > The magnitude of the deviation from -1 (only 0.000002) is almost certainly > due > to rounding errors and is nothing serious in this case. > > -Justin > > -- > ======================================== > > 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 list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 81, Issue 104 > ****************************************** >
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