[gmx-developers] Group cutoff-scheme simulation temperature affected by nh-chain-length
Mark Abraham
mark.j.abraham at gmail.com
Fri Nov 3 02:24:32 CET 2017
Hi,
On Fri, Nov 3, 2017 at 2:12 AM Du, Yu <duyu at sioc.ac.cn> wrote:
> Hi Mark and Dear GMX-Developers,
>
> I tried the gmx check -s1 -s2, it gives comparison each recording steps.
>
That sounds like your comparing the trajectories. I intended you to compare
the .tpr files, because the combinations are computed in that. Yours may
differ.
> But I need the reason of not changing comb-rule 2to1 and sigma,epsilon to
> c6,c12 in amber ff.
>
> Could you explain why the combined parameters are different and whose
> combined parameters are different from?
>
See the equations in section 5.3.2 of the reference manual. Only in some
cases with the parameters for a pair of atom types be the same in the two
rules. Whether that applies is up to you, but if so then the gmx compare
will confirm your deduction.
> I have adapted the sigma and epsilon of ffnonbonded.itp to c6 and
> c12, comb-rule 2 to 1, I think it's reasonable and these places (forcefield.itp
> and ffnonbonded.itp) are where one only needs to adapt.
>
In so doing, you surely assumed that you were treating an A-A interaction.
But the A-B interactions are the relevant ones for *combining* parameters.
> But Prof. Hess said I should never change the comb-rule of ff. Thanks for
> any detailed information.
>
Because it does not work for e.g. proteins.
Mark
> Best,
> Yu
>
>
> -----Original Messages-----
> *From:*"Mark Abraham" <mark.j.abraham at gmail.com>
> *Sent Time:*2017-11-02 22:52:54 (Thursday)
> *To:* gmx-developers at gromacs.org
> *Cc:* GMX-developer <gromacs.org_gmx-developers at maillist.sys.kth.se>
>
>
> *Subject:* Re: [gmx-developers] Group cutoff-scheme simulation
> temperature affected by nh-chain-length
>
> Hi,
>
> The general reason is that the combined parameters are different. Whether
> that matters depends on your system composition. You can see if that
> affects you by doing gmx compare -s1 -s2
>
> Mark
>
> On Thu, Nov 2, 2017 at 3:42 PM Du, Yu <duyu at sioc.ac.cn> wrote:
>
>> Dear Prof. Hess,
>>
>> I compared the MD results of comb-rule=1 and 2 amber99sb-ildn ff and
>> found that there is little difference between them. The MD results of
>> original amber ff and adapted are pasted in the end of this email.
>>
>> Could you give the reason that change should never be made to the
>> comb-rule and the coorsponding ffnonbonded.itp file?
>>
>> Thanks a lot.
>>
>> Regards,
>> Yu
>>
>> ##########################original amber ff############################
>> Statistics over 25001 steps using 251 frames
>>
>> Energies (kJ/mol)
>> Angle Proper Dih. Improper Dih. LJ-14
>> Coulomb-14
>> 4.02507e+03 5.15818e+03 2.75373e+02 2.11916e+03
>> 1.69171e+04
>> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic
>> En.
>> 6.20228e+04 -5.36969e+05 3.15506e+03 -4.43296e+05
>> 8.45579e+04
>> Total Energy Conserved En. Temperature Pressure (bar) Constr.
>> rmsd
>> -3.58738e+05 -4.39556e+05 3.00296e+02 -1.81660e+02
>> 0.00000e+00
>>
>> Total Virial (kJ/mol)
>> 3.01440e+04 1.75821e+01 -1.58821e+01
>> 1.84730e+01 3.00339e+04 -9.97169e+01
>> -1.46410e+01 -1.00240e+02 3.00330e+04
>>
>> Pressure (bar)
>> -1.84467e+02 -3.37456e+00 2.10386e+00
>> -3.46046e+00 -1.75964e+02 1.04734e+01
>> 1.98421e+00 1.05238e+01 -1.84549e+02
>>
>> T-Protein T-non-Protein
>> 2.99844e+02 3.00324e+02
>>
>>
>> M E G A - F L O P S A C C O U N T I N G
>>
>> NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
>> RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
>> W3=SPC/TIP3p W4=TIP4p (single or pairs)
>> V&F=Potential and force V=Potential only F=Force only
>>
>> Computing: M-Number M-Flops %
>> Flops
>>
>> -----------------------------------------------------------------------------
>> Pair Search distance check 14291.569978 128624.130 0.5
>> NxN Ewald Elec. + LJ [F] 184675.631168 12188591.657 51.1
>> NxN Ewald Elec. + LJ [V&F] 2250.700664 240824.971 1.0
>> NxN Ewald Elec. [F] 160299.489552 9778268.863 41.0
>> NxN Ewald Elec. [V&F] 1953.462840 164090.879 0.7
>> 1,4 nonbonded interactions 127.655106 11488.960 0.0
>> Calc Weights 2540.801628 91468.859 0.4
>> Spread Q Bspline 54203.768064 108407.536 0.5
>> Gather F Bspline 54203.768064 325222.608 1.4
>> 3D-FFT 69761.190336 558089.523 2.3
>> Solve PME 48.401936 3097.724 0.0
>> Reset In Box 42.311124 126.933 0.0
>> CG-CoM 42.412752 127.238 0.0
>> Angles 88.678547 14897.996 0.1
>> Propers 139.355574 31912.426 0.1
>> Impropers 10.650426 2215.289 0.0
>> Virial 10.413396 187.441 0.0
>> Stop-CM 8.536752 85.368 0.0
>> Calc-Ekin 169.413876 4574.175 0.0
>> Lincs 165.281870 9916.912 0.0
>> Lincs-Mat 3504.083832 14016.335 0.1
>> Constraint-V 1040.480273 8323.842 0.0
>> Constraint-Vir 12.528823 300.692 0.0
>> Settle 583.493470 188468.391 0.8
>>
>> -----------------------------------------------------------------------------
>> Total 23873328.747 100.0
>> ##########################original amber ff############################
>>
>> ##########################comb-rule=1 amber ff############################
>> Statistics over 25001 steps using 251 frames
>>
>> Energies (kJ/mol)
>> Angle Proper Dih. Improper Dih. LJ-14
>> Coulomb-14
>> 4.01117e+03 5.20573e+03 2.78324e+02 2.02413e+03
>> 1.68747e+04
>> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic
>> En.
>> 6.22595e+04 -5.37413e+05 3.13120e+03 -4.43628e+05
>> 8.45492e+04
>> Total Energy Conserved En. Temperature Pressure (bar) Constr.
>> rmsd
>> -3.59079e+05 -4.40129e+05 3.00265e+02 -1.82026e+02
>> 0.00000e+00
>>
>> Total Virial (kJ/mol)
>> 3.01455e+04 -9.34378e+01 -1.54004e+02
>> -9.20285e+01 3.00302e+04 -4.38835e+01
>> -1.53975e+02 -4.42383e+01 3.00377e+04
>>
>> Pressure (bar)
>> -1.89288e+02 8.10551e+00 1.64126e+01
>> 7.96965e+00 -1.76137e+02 7.49214e-01
>> 1.64098e+01 7.83424e-01 -1.80654e+02
>>
>> T-Protein T-non-Protein
>> 3.00317e+02 3.00262e+02
>>
>>
>> M E G A - F L O P S A C C O U N T I N G
>>
>> NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
>> RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
>> W3=SPC/TIP3p W4=TIP4p (single or pairs)
>> V&F=Potential and force V=Potential only F=Force only
>>
>> Computing: M-Number M-Flops %
>> Flops
>>
>> -----------------------------------------------------------------------------
>> Pair Search distance check 14608.461222 131476.151 0.6
>> NxN Ewald Elec. + LJ [F] 183977.095776 12142488.321 51.1
>> NxN Ewald Elec. + LJ [V&F] 2242.460760 239943.301 1.0
>> NxN Ewald Elec. [F] 159476.727584 9728080.383 40.9
>> NxN Ewald Elec. [V&F] 1943.414296 163246.801 0.7
>> 1,4 nonbonded interactions 127.655106 11488.960 0.0
>> Calc Weights 2540.801628 91468.859 0.4
>> Spread Q Bspline 54203.768064 108407.536 0.5
>> Gather F Bspline 54203.768064 325222.608 1.4
>> 3D-FFT 69761.190336 558089.523 2.3
>> Solve PME 48.401936 3097.724 0.0
>> Reset In Box 42.345000 127.035 0.0
>> CG-CoM 42.412752 127.238 0.0
>> Angles 88.678547 14897.996 0.1
>> Propers 139.355574 31912.426 0.1
>> Impropers 10.650426 2215.289 0.0
>> Virial 10.413396 187.441 0.0
>> Stop-CM 8.536752 85.368 0.0
>> Calc-Ekin 169.413876 4574.175 0.0
>> Lincs 168.515866 10110.952 0.0
>> Lincs-Mat 3570.772848 14283.091 0.1
>> Constraint-V 1043.984536 8351.876 0.0
>> Constraint-Vir 12.566057 301.585 0.0
>> Settle 583.673648 188526.588 0.8
>>
>> -----------------------------------------------------------------------------
>> Total 23778711.227 100.0
>> ##########################comb-rule=1 amber ff############################
>>
>> -----Original Messages-----
>> *From:*"Du, Yu" <duyu at sioc.ac.cn>
>>
>> *Sent Time:*2017-11-02 19:45:40 (Thursday)
>>
>>
>> *To:* GMX-developer <gromacs.org_gmx-developers at maillist.sys.kth.se>
>> *Cc:*
>> *Subject:* Re: [gmx-developers] Group cutoff-scheme simulation
>> temperature affected by nh-chain-length
>>
>> Thanks for Prof. Berk's prompt fix.
>>
>> You advised that "You should never change the combination rule of a force
>> field" in Bug #2286 <https://redmine.gromacs.org/issues/2286> and
>> because tabulized potential needs comb-rule=1, what should I do to use the
>> amber99sb-ildn ff? (ff needed for protein-ligand simulation system) Or in
>> Gromacs, I can only use the group cutoff-scheme and tabulized potential
>> with gromos ff?
>>
>> Could you please explain the consequence I may get when I use the
>> comb-func=1 amber99sb-ildn ff which is changed by myself?
>>
>> Best,
>> Yu
>>
>> -----Original Messages-----
>> *From:*"Du, Yu" <duyu at sioc.ac.cn>
>> *Sent Time:*2017-11-02 14:00:40 (Thursday)
>> *To:* GMX-developer <gromacs.org_gmx-developers at maillist.sys.kth.se>
>> *Cc:*
>> *Subject:* Re: [gmx-developers] Group cutoff-scheme simulation
>> temperature affected by nh-chain-length
>>
>> Dear GMX-Developers and Shirts,
>>
>> To reproduce the the problem, I use the material in GROMACS Tutorials Lysozyme
>> in Water
>> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html>
>> .
>>
>> Yes, Prof. Shirts. If I use standard vdwtype=cut-off, coulombtype=pme and
>> cutoff-scheme=group, the simulation temperature accords with the ref_t.
>> If I use gromos ff and tabulized potential, there is no temperature
>> problem.
>>
>> Now the problem is pinned on the relation between tabulized potential and
>> thermostat under amber99sb-ildn ff.
>>
>> I filed Bug #2286 in redmine.
>> https://redmine.gromacs.org/issues/2286
>>
>> Hope you could give some advice about this issue.
>>
>> Yu
>>
>> -----Original Messages-----
>> *From:*"Michael R Shirts" <Michael.Shirts at Colorado.EDU>
>> *Sent Time:*2017-10-23 19:43:38 (Monday)
>> *To:* "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>,
>> GMX-developer <gromacs.org_gmx-developers at maillist.sys.kth.se>
>> *Cc:*
>> *Subject:* Re: [gmx-developers] Group cutoff-scheme simulation
>> temperature affected by nh-chain-length
>>
>> If you can file a bug report in redmine (http://redmine.gromacs.org/)
>> with example files, that would be useful. Before you file it can you check
>> if problem happens if you use standard cutoffs, instead of tabulated
>> cutoffs? I wonder if there is some sort of code path that it’s going down.
>> I will bet that combination of inputs has only very rarely been used.
>> Also, you said the temperature jumps. Does it come back down to 310, or
>> does it stay there?
>>
>>
>>
>> Generally, I would recommend using v-rescale instead of Nose-Hoover.
>> Nose-Hoover has some known flaws; increasing the chain length is supposed
>> to help things, but doesn’t really help that much for realistic systems,
>> just with very simple ones.
>>
>>
>>
>> However, any Nose-Hoover change length should in principle give the same
>> average, and did when the code was written. If it doesn’t, the code was
>> broken somewhere, possibly because of lack of coverage in the regression
>> tests and something getting out of sync.
>>
>>
>>
>> Best,
>>
>> ~~~~~~~~~~~~~~~~
>>
>> Michael Shirts
>>
>> Associate Professor
>>
>> michael.shirts at colorado.edu
>>
>> http://www.colorado.edu/lab/shirtsgroup/
>>
>> Phone: (303) 735-7860
>>
>> Office: JSCBB C123
>>
>> Department of Chemical and Biological Engineering
>>
>> University of Colorado Boulder
>>
>>
>>
>> *From: *<gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> on
>> behalf of "Du, Yu" <duyu at sioc.ac.cn>
>> *Reply-To: *"gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
>> *Date: *Monday, October 23, 2017 at 12:48 AM
>> *To: *GMX-developer <gromacs.org_gmx-developers at maillist.sys.kth.se>
>> *Subject: *[gmx-developers] Group cutoff-scheme simulation temperature
>> affected by nh-chain-length
>>
>>
>>
>> Dear GMX Developer and Prof. Hess,
>>
>>
>>
>> I think this question is not common to GMX users, so I post it here.
>>
>>
>>
>> Prof. Hess is very familiar with the tabulized potential and group cutoff
>> scheme, so I also CC this email to you. Any advice will be appreciated.
>>
>>
>>
>> The Backgroud:
>>
>> I simulated protein-ligand system (ref_t=300) with amber99sb-ildn ff. I
>> used the normal table6-12.xvg tabulized potential to reproduce this problem.
>>
>>
>>
>> The Problem:
>>
>> In NVT simulation, integrator=md-vv, Tcoupl=nose-hoover, coulombtype=pme-user,
>> vdwtype=user. I found that at the start of the simulation, there is a
>> temperature jump to around 310K (average 310K in 100ps) higher than the
>> ref_t (300K) under nh-chain-length=10.
>>
>>
>>
>> 1)I tuned and spotted the nh-chain-length parameter. If I
>> used nh-chain-length=1 there is no temperature jump and temperature can
>> converge very well to 300K.
>>
>>
>>
>> 2)I replicated the same experiment in verlet scheme, the temperature
>> converged to ref_t 300K in 100ps and no jump in nh-chain-length=2, which
>> can 50K temperature jump (to 350K).
>>
>>
>>
>> The Question:
>>
>> 1)How will the nh-chain-length parameter affect the simulation
>> temperature under the group cut-off scheme?
>>
>> 2)Is it valid to use NH (nh-chain-length=1) not NH chain
>> (nh-chain-length>1) to simulate the protein-ligand system?
>>
>>
>>
>> Thanks for any advice.
>>
>>
>>
>> --
>>
>> Du, Yu
>> PhD Student,
>> Shanghai Institute of Organic Chemistry
>>
>> 345 Ling Ling Rd., Shanghai, China.
>>
>> Zip: 200032, Tel: (86) 021 5492 5275
>>
>> --
>> Gromacs Developers mailing list
>>
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>> posting!
>>
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>
>
> --
> Du, Yu
> PhD Student,
> Shanghai Institute of Organic Chemistry
> 345 Ling Ling Rd., Shanghai, China.
> Zip: 200032, Tel: (86) 021 5492 5275
> --
> Gromacs Developers mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> or send a mail to gmx-developers-request at gromacs.org.
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