[gmx-users] Re: gmx-users Digest, Vol 81, Issue 130
Xiaohu Li
xiaohuli914 at gmail.com
Wed Jan 19 23:40:31 CET 2011
> Message: 2
> Date: Wed, 19 Jan 2011 23:23:12 +0100
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] RE: Important: Bugs in NEMD calculation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <COL113-W651FF8B51B6E10B91E0E4F8EF60 at phx.gbl>
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>
>
>
>
> It seems you are right.
> The density is calculated a few lines before 1/visc is stored, but it is
> not being used.
> Strange that this always went unnoticed, since it already seems to have
> been wrong in 4.0.
> The density of water is so close to 1000 that you wouldn't notice the
> difference
>
> But in a quick test I don't get the correct viscosity either way.
> I will have to find time for a thorough check.
> Do you get the right answer by dividing by the missing density term in
> src/mdlib/mdebin.c?
>
> Berk
>
Well, my force field can not reproduce the experiment anyway.
However, the wrong way of calculating in NEMD(vol instead of dens) is
getting visocisty much much lower than what I got from using g_energy -vis.
If I'm understanding correctly, the one with visco.xvg(column 1 vs column 2)
should be the one I'm supposed to look at, even with 12ns simulation, this
does not converge, but roughly speaking the NEMD results with the vol
replaced by rho(I wrote a outside script to calculate this) is on the same
order of magnitude as the g_energy -vis using green-kudo(is that right?)
expression.
Xiaohu
>
> Date: Wed, 19 Jan 2011 14:48:32 -0600
> From: xiaohuli914 at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] RE: Important: Bugs in NEMD calculation
>
>
>
> Date: Wed, 19 Jan 2011 20:43:20 +0100
>
> From: Berk Hess <gmx3 at hotmail.com>
>
> Subject: RE: [gmx-users] Important: Bugs in NEMD calculation
>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
> Message-ID: <COL113-W2019E7174AFFBAEF819A1A8EF60 at phx.gbl>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
>
>
>
>
>
>
> > Date: Wed, 19 Jan 2011 19:13:12 +0100
>
> > From: spoel at xray.bmc.uu.se
>
> > To: gmx-users at gromacs.org
>
> > Subject: Re: [gmx-users] Important: Bugs in NEMD calculation
>
> >
>
> > On 2011-01-19 18.36, Xiaohu Li wrote:
>
> > > Hi, All,
>
> > > I've found a bug in the NEMD calculation for viscosity. This has
>
> > > been reviewed in /*Hess's paper at JCP 116 209 2002.*/
>
> > > The version of gromacs I'm using is the development version.
>
> > > Notice that this version correct a previous but of 4.5.3, where you
> uses
>
> > > NEMD, both the term V(eq. 21 on Hess's paper) and 1/eta(shear viscosity
>
> > > inverse) are supposed to be written to the *.edr file, however,
>
> > > the 4.5.3 versions does not have this. This version can be retrieved at
>
> > >
> http://repo.or.cz/w/gromacs.git/commit/c83de86d65ce7135be6cef15e9100d7516e6d9a7
>
> > > *However, even this version is buggy since eta=A*rho/(V*k**2)(eq. 20
>
> > > Hess's paper)*. *I have performed simulation and has found out that the
>
> > > V and eta which are written in *edr file does not match according to
> the
>
> > > formula, a little further check on the source code mdebin.c under the
>
> > > directory src/mdlib shows that it is actually calculating
>
> > > eta=A*Volume/(V*k**2) where density of rho should have been used. (This
>
> > > is at line 755 of mdebin.c ).
>
> > > I hope everyone who is using this can be aware of this, if you
> ever
>
> > > used this code to produce data, the V is correct from *edr, however,
> you
>
> > > need to manuelly get your eta using the above formula.
>
> > > For the GMX developers, I hope anyone of you can correct this bug.
>
> > >
>
>
>
> I fixed this bug recently is the git release-4-5-patches branch.
>
> You can get the fix from git and it will be in the 4.5.4 release
>
> (no date yet).
> Which one are you referring to? The one I got is the one you uploaded that
> fixed the zero viscosity and 2*cosZ*vel-x in edr file.
> This bug refers the wrong calculation of 1/eta.
>
>
>
>
>
> > Thanks for pointing that out. There also is a small issue in that the
>
> > volume is computed for a rectangular box
>
> > vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
>
> > dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
>
> >
>
> > which would be incorrect for a non-rectangular box. You should however
>
> > use a rectangular box for this kind of calculations, although this is
>
> > not enforced by grompp.
>
>
>
> No.
>
> That formula is correct for any triclinic box!
>
>
>
> Berk
>
>
>
> >
>
> > >
>
> > >
>
> > > Xiaohu
>
> > > *
>
> > >
>
> >
>
> >
>
> > --
>
> > David van der Spoel, Ph.D., Professor of Biology
>
> > Dept. of Cell & Molec. Biol., Uppsala University.
>
> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>
> > spoel at xray.bmc.uu.se http://folding.bmc.uu.se
>
> > --
>
> > gmx-users mailing list gmx-users at gromacs.org
>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>
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> Message: 3
> Date: Wed, 19 Jan 2011 17:29:02 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] CNT
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D3765AE.6080307 at vt.edu>
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>
> trevor brown wrote:
> > Dear Justin,
> > Regarding our previous discussion under "CNT" topic, you want to know
> > exactly what I did to define C-C interaction. I have summarized it below.
> >
> > 1. I copied oplsaa.ff folder in my working directory
> > 2. I added following lines to atomname2type.n2t
> > C opls_995 0 12.011 2 C 0.142 C 0.142
> > C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142
> > C opls_997 0 12.011 4 C 0.142 C 0.142 C 0.142 C 0.142
> > C opls_998 0 12.011 5 C 0.142 C 0.142 C 0.142 C 0.142
> > C 0.142
> > 3. I added those to atomtypes.atp
> > opls_995 12.01100 ;
> > opls_996 12.01100 ;
> > opls_997 12.01100 ;
> > opls_998 12.01100 ;
> >
> > 4. I added those to ffbonded.itp
> > [ bondtypes ]
> > C C 1 0.14210 478900
> > [ angletypes ]
> > C C C 1 120.000 562.2
> > [ dihedraltypes ]
> > 5. I constructed .top file for CNT with the following, then I converted
> > it into .itp by vi editor
> > g_x2top -f cnt.gro -o cnt.top -nopairs -nexcl 5
> > 6. By pdb2gmx, I obtained .top for peptide then I converted it into .itp
> > 7. I combined CNT and peptide's pdbs in pymol and saved.
> > 8. I wrote a .top file given below,
> > ;
> > ; File 'topol.top' was generated
> > ; By user: onbekend (0)
> > ; On host: onbekend
> > ; At date: Mon Jan 10 02:51:19 2011
> > ;
> > ; This is a standalone topology file
> > ;
> > ; It was generated using program:
> > ; pdb2gmx - VERSION 4.5.3
> > ;
> > ; Command line was:
> > ; pdb2gmx -ignh -f vpgvg10.pdb
> > ;
> > ; Force field was read from the standard Gromacs share directory.
> > ;
> > ; Include forcefield parameters
> > #include "forcefield.itp"
> >
>
> Be careful with this - if you move this topology between directories, it
> will
> call any forcefield.itp file that may be in the working directory. What
> did you
> remove the "oplsaa.ff" prefix?
>
> > ; Include topology for CNT
> > #include "cnt.itp"
> > ; Include topology for UW1
> > #include "uw1.itp"
> > ; Include water topology
> > #include "spc.itp"
> > [ system ]
> > ; Name
> > Protein and CNT in water
> > [ molecules ]
> > ; Compound #mols
> > Protein 1
> > CNT 1
> > SOL 4019
> > 9. When I make grompp for minimization it givea me the following error
> > WARNING 1 [file ffbonded.itp, line 2703]:
> > Overriding Bond parameters.
> > old: 0.151 292880 0.151 292880
> > new: C C 1 0.14210 478900
> >
> > ERROR 1 [file ffbonded.itp, line 2707]:
> > Not enough parameters
> > Generated 334153 of the 334153 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 0.5
> > Generated 334153 of the 334153 1-4 parameter combinations
> > -------------------------------------------------------
> > Program grompp, VERSION 4.5.3
> > Source code file: toppush.c, line: 1166
> > Fatal error:
> > Atomtype opls_996 not found
> >
> > That is all what I exactly did. Is anything wrong or missing?
> >
>
> You never defined nonbonded parameters for your new atom type. You've
> declared
> that it exists in the .atp file, but then you didn't add that atom type in
> ffnonbonded.itp.
>
> -Justin
>
> > best wishes
> > trevor
> >
> >
> >
> >
>
> --
> ========================================
>
> 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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