[gmx-users] Re:Viscosity calculations
Xiaohu Li
xiaohuli914 at gmail.com
Mon Jan 17 20:20:53 CET 2011
On Mon, Jan 17, 2011 at 8:29 AM, <gmx-users-request at gromacs.org> wrote:
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> 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 <erikm at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Non integral charges
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D3430BB.20207 at xray.bmc.uu.se>
> 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
> erikm at xray.bmc.uu.se http://folding.bmc.uu.se/
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 17 Jan 2011 07:07:51 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Non integral charges
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D343117.2070005 at vt.edu>
> 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" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Viscosity calculations
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D3431F1.8070203 at vt.edu>
> 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 <hmkvsri at gmail.com>
> Subject: Re: [gmx-users] Non integral charges
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTins7nzCkP-kk0o+84f=OeD7rj2jKYfEiH9dQOmT at mail.gmail.com>
> 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 <jalemkul at vt.edu> 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 gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
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> ------------------------------
>
> Message: 5
> Date: Mon, 17 Jan 2011 14:45:37 +0100
> From: "K. Singhal" <k.singhal at uva.nl>
> Subject: [gmx-users] Secondary structure loss in implicit solvent
> simulations
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <9C8B103A-1757-4A3E-B7E2-3A7B5E223201 at uva.nl>
> 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 <vvchaban at gmail.com>
> Subject: [gmx-users] Re: Non integral charges
> To: gmx-users at gromacs.org
> Message-ID:
> <AANLkTimFLitXcgEhOTucxm1ERau57C9EaEMCiyiK4c+- at mail.gmail.com<AANLkTimFLitXcgEhOTucxm1ERau57C9EaEMCiyiK4c%2B- at mail.gmail.com>
> >
> 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" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: Non integral charges
> To: vvchaban at gmail.com, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <4D34521C.6000705 at vt.edu>
> 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
>
> ========================================
>
>
> ------------------------------
>
> --
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> End of gmx-users Digest, Vol 81, Issue 104
> ******************************************
>
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