[gmx-users] Re: frustrating NVE (David)
David
spoel at xray.bmc.uu.se
Fri Nov 11 20:15:13 CET 2005
On Sat, 2005-11-12 at 01:01 +0800, Xiaobing Feng wrote:
> Thanks David,
>
> I tried with shifted vdw, and it did give me good E-conservation.
> I don't know how shifted vdw would effect the properies of system, I've
> been working on that force field using cut-off for LJ.
> I tried with longer cut-off, 1.6 for rlist, rvdw, and rcoulomb. Energy
> is much better, it's decreasing slowly, still not good for long time simulation though.
> With DLPOLY the E-conservation is always very good even though I use only 1.1 for LJ cut-off.
> I shifted from DLPOLY to gromacs, since gromacs is really much faster.
> Do you know of other ways for GROMACS that could keep E well conserved with LJ cuf-off scheme?
Are you certain that DLPOLY does not shift the forces either?
Check the source, don't trust the manual.
It could also be due to the size of your charge groups, the tolerance
for constraints and the use (or not) of double precision.
>
>
> Many thanks
> Xiaobing
>
> --- gmx-users-request at gromacs.org wrote:
> > Send gmx-users mailing list submissions to
> > gmx-users at gromacs.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > or, via email, send a message with subject or body 'help' to
> > gmx-users-request at gromacs.org
> >
> > You can reach the person managing the list at
> > gmx-users-owner at gromacs.org
> >
> >
> > Message: 4
> > Date: Fri, 11 Nov 2005 06:42:02 +0800 (CST)
> > From: Xiaobing Feng <xbfeng05 at yahoo.com.cn>
> > Subject: [gmx-users] frustrating NVE
> > To: gmx-users at gromacs.org
> > Message-ID: <20051110224203.41381.qmail at web15601.mail.cnb.yahoo.com>
> > Content-Type: text/plain; charset=gb2312
> >
> > Dear everyone,
> >
> > I did a MD NVE run. The total energy is going up nearly linearly,
> > total energy went from -46000 kJ/mol to -45700 kJ/mol after 450 ps, and no sign
> > to level off. There is no close contacts in the conf.gro, and the run is pretty
> > long, the system should be equilibrated long ago. The system is made of a solid
> > and its melt, an interfacial system.
> > The main setting is :
> > dt =1fs, Coulombtype=PME, rlist = rvdw = rcoulomb=1.2, fourierspacing=0.1,
> > pme_order=4, ewald_rtol=1e-5
> > There is one H atom, O-H bond is contrainted by Lincs.
> > Given in the following is the complete mdout.mdp ( I removed comments only).
> > Could anybody tell me what's wrong with my setting?
> >
> > Thanks a lot.
> >
> > Xiaobing
> > ---------------mdout.mdp -----------------------
> >
> >
> > cpp = /usr/bin/cpp
> > include =
> > define =
> > integrator = md
> > tinit = 0
> > dt = 0.001
> > nsteps = 500000
> > init_step = 0
> > comm-mode = Linear
> > nstcomm = 1
> > comm-grps =
> >
> > bd-fric = 0
> > ld-seed = 1993
> >
> > emtol = 10
> > emstep = 0.01
> > nstcgsteep = 1000
> > nbfgscorr = 10
> >
> > nstxout = 1000
> > nstvout = 1000
> > nstfout = 1000
> > nstcheckpoint = 10000
> > nstlog = 1000
> > nstenergy = 100
> > nstxtcout = 2000
> > xtc-precision = 10000
> > xtc-grps =
> > energygrps =
> >
> > nstlist = 1
> > ns_type = grid
> > pbc = xyz
> > rlist = 1.2
> > domain-decomposition = no
> >
> > coulombtype = PME
> > rcoulomb-switch = 0
> > rcoulomb = 1.2
> > epsilon_r = 1
> > epsilon_rf = 1
> > vdw-type = Cut-off
> > rvdw-switch = 0
> > rvdw = 1.2
> > DispCorr = EnerPres
> > table-extension = 1
> > energygrp_table =
> > fourierspacing = 0.1
> > fourier_nx = 0
> > fourier_ny = 0
> > fourier_nz = 0
> > pme_order = 4
> > ewald_rtol = 1e-05
> > ewald_geometry = 3d
> > epsilon_surface = 0
> > optimize_fft = no
> >
> > gb_algorithm = Still
> > nstgbradii = 1
> > rgbradii = 2
> > gb_saltconc = 0
> >
> > implicit_solvent = No
> >
> > Tcoupl = no
> > tc-grps = System
> > tau_t = 0.1
> > ref_t = 309
> > Pcoupl = no
> > Pcoupltype = semiisotropic
> > tau_p = 2.0
> > compressibility = 4.4395e-5 4.4395e-5
> > ref_p = 1.01325 1.01325
> > andersen_seed = 815131
> >
> > QMMM = no
> > QMMM-grps =
> > QMmethod =
> > QMMMscheme = normal
> > QMbasis =
> > QMcharge =
> > QMmult =
> > SH =
> > CASorbitals =
> > CASelectrons =
> > SAon =
> > SAoff =
> > SAsteps =
> > MMChargeScaleFactor = 1
> > bOPT =
> > bTS =
> >
> > annealing =
> > annealing_npoints =
> > annealing_time =
> > annealing_temp =
> >
> > gen_vel = yes
> > gen_temp = 309
> > gen_seed = 1993
> >
> > constraints = hbonds
> > constraint-algorithm = Lincs
> > unconstrained-start = no
> > Shake-SOR = no
> > shake-tol = 1e-04
> > lincs-order = 5
> > lincs-iter = 2
> > lincs-warnangle = 30
> > morse = no
> >
> > energygrp_excl =
> >
> > disre = No
> > disre-weighting = Conservative
> > disre-mixed = no
> > disre-fc = 1000
> > disre-tau = 0
> > nstdisreout = 100
> > orire = no
> > orire-fc = 0
> > orire-tau = 0
> > orire-fitgrp =
> > nstorireout = 100
> > dihre = No
> > dihre-fc = 1000
> > dihre-tau = 0
> > nstdihreout = 100
> >
> > free-energy = no
> > init-lambda = 0
> > delta-lambda = 0
> > sc-alpha = 0
> > sc-power = 1
> > sc-sigma = 0.3
> >
> > acc-grps =
> > accelerate =
> > freezegrps =
> > freezedim =
> > cos-acceleration = 0
> > deform =
> >
> > E-x =
> > E-xt =
> > E-y =
> > E-yt =
> > E-z =
> > E-zt =
> >
> > user1-grps =
> > user2-grps =
> > userint1 = 0
> > userint2 = 0
> > userint3 = 0
> > userint4 = 0
> > userreal1 = 0
> > userreal2 = 0
> > userreal3 = 0
> > userreal4 = 0
> >
> >
> >
> >
> >
> >
> >
> > ___________________________________________________________
> > 雅虎免费G邮箱－中国第一绝无垃圾邮件骚扰超大邮箱
> > http://cn.mail.yahoo.com
> >
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Fri, 11 Nov 2005 08:33:41 +0100
> > From: David <spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-users] frustrating NVE
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID:
> > <1131694421.4543.0.camel at 217-208-143-88-o1123.tbon.telia.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > On Fri, 2005-11-11 at 06:42 +0800, Xiaobing Feng wrote:
> > > Dear everyone,
> > >
> > > I did a MD NVE run. The total energy is going up nearly linearly,
> > > total energy went from -46000 kJ/mol to -45700 kJ/mol after 450 ps, and no sign
> > > to level off. There is no close contacts in the conf.gro, and the run is pretty
> > > long, the system should be equilibrated long ago. The system is made of a solid
> > > and its melt, an interfacial system.
> > > The main setting is :
> > > dt =1fs, Coulombtype=PME, rlist = rvdw = rcoulomb=1.2, fourierspacing=0.1,
> > > pme_order=4, ewald_rtol=1e-5
> > > There is one H atom, O-H bond is contrainted by Lincs.
> > > Given in the following is the complete mdout.mdp ( I removed comments only).
> > > Could anybody tell me what's wrong with my setting?
> > You may want to use a shifted Vdw potential, e.g. from 1.0 to 1.2 nm
> >
> > >
> > > Thanks a lot.
> > >
> > > Xiaobing
> > > ---------------mdout.mdp -----------------------
> > >
> > >
> > > cpp = /usr/bin/cpp
> > > include =
> > > define =
> > > integrator = md
> > > tinit = 0
> > > dt = 0.001
> > > nsteps = 500000
> > > init_step = 0
> > > comm-mode = Linear
> > > nstcomm = 1
> > > comm-grps =
> > >
> > > bd-fric = 0
> > > ld-seed = 1993
> > >
> > > emtol = 10
> > > emstep = 0.01
> > > nstcgsteep = 1000
> > > nbfgscorr = 10
> > >
> > > nstxout = 1000
> > > nstvout = 1000
> > > nstfout = 1000
> > > nstcheckpoint = 10000
> > > nstlog = 1000
> > > nstenergy = 100
> > > nstxtcout = 2000
> > > xtc-precision = 10000
> > > xtc-grps =
> > > energygrps =
> > >
> > > nstlist = 1
> > > ns_type = grid
> > > pbc = xyz
> > > rlist = 1.2
> > > domain-decomposition = no
> > >
> > > coulombtype = PME
> > > rcoulomb-switch = 0
> > > rcoulomb = 1.2
> > > epsilon_r = 1
> > > epsilon_rf = 1
> > > vdw-type = Cut-off
> > > rvdw-switch = 0
> > > rvdw = 1.2
> > > DispCorr = EnerPres
> > > table-extension = 1
> > > energygrp_table =
> > > fourierspacing = 0.1
> > > fourier_nx = 0
> > > fourier_ny = 0
> > > fourier_nz = 0
> > > pme_order = 4
> > > ewald_rtol = 1e-05
> > > ewald_geometry = 3d
> > > epsilon_surface = 0
> > > optimize_fft = no
> > >
> > > gb_algorithm = Still
> > > nstgbradii = 1
> > > rgbradii = 2
> > > gb_saltconc = 0
> > >
> > > implicit_solvent = No
> > >
> > > Tcoupl = no
> > > tc-grps = System
> > > tau_t = 0.1
> > > ref_t = 309
> > > Pcoupl = no
> > > Pcoupltype = semiisotropic
> > > tau_p = 2.0
> > > compressibility = 4.4395e-5 4.4395e-5
> > > ref_p = 1.01325 1.01325
> > > andersen_seed = 815131
> > >
> > > QMMM = no
> > > QMMM-grps =
> > > QMmethod =
> > > QMMMscheme = normal
> > > QMbasis =
> > > QMcharge =
> > > QMmult =
> > > SH =
> > > CASorbitals =
> > > CASelectrons =
> > > SAon =
> > > SAoff =
> > > SAsteps =
> > > MMChargeScaleFactor = 1
> > > bOPT =
> > > bTS =
> > >
> > > annealing =
> > > annealing_npoints =
> > > annealing_time =
> > > annealing_temp =
> > >
> > > gen_vel = yes
> > > gen_temp = 309
> > > gen_seed = 1993
> > >
> > > constraints = hbonds
> > > constraint-algorithm = Lincs
> > > unconstrained-start = no
> > > Shake-SOR = no
> > > shake-tol = 1e-04
> > > lincs-order = 5
> > > lincs-iter = 2
> > > lincs-warnangle = 30
> > > morse = no
> > >
> > > energygrp_excl =
> > >
> > > disre = No
> > > disre-weighting = Conservative
> > > disre-mixed = no
> > > disre-fc = 1000
> > > disre-tau = 0
> > > nstdisreout = 100
> > > orire = no
> > > orire-fc = 0
> > > orire-tau = 0
> > > orire-fitgrp =
> > > nstorireout = 100
> > > dihre = No
> > > dihre-fc = 1000
> > > dihre-tau = 0
> > > nstdihreout = 100
> > >
> > > free-energy = no
> > > init-lambda = 0
> > > delta-lambda = 0
> > > sc-alpha = 0
> > > sc-power = 1
> > > sc-sigma = 0.3
> > >
> > > acc-grps =
> > > accelerate =
> > > freezegrps =
> > > freezedim =
> > > cos-acceleration = 0
> > > deform =
> > >
> > > E-x =
> > > E-xt =
> > > E-y =
> > > E-yt =
> > > E-z =
> > > E-zt =
> > >
> > > user1-grps =
> > > user2-grps =
> > > userint1 = 0
> > > userint2 = 0
> > > userint3 = 0
> > > userint4 = 0
> > > userreal1 = 0
> > > userreal2 = 0
> > > userreal3 = 0
> > > userreal4 = 0
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > ___________________________________________________________
> > >
> 璐G��锛涓界�涓沌鹃�欢楠拌澶ч��
>
> > > http://cn.mail.yahoo.com
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> >
> >
> > End of gmx-users Digest, Vol 19, Issue 38
> > *****************************************
> >
>
>
>
>
>
>
>
> ___________________________________________________________
> 雅虎免费G邮箱－中国第一绝无垃圾邮件骚扰超大邮箱
> http://cn.mail.yahoo.com
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
More information about the gromacs.org_gmx-users
mailing list