[gmx-users] Re: frustrating NVE (David)
Xiaobing Feng
xbfeng05 at yahoo.com.cn
Fri Nov 11 18:01:25 CET 2005
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?
Many thanks
Xiaobing
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> 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
>
>
>
>
>
>
>
> ___________________________________________________________
> ÑÅ»¢Ãâ·ÑGÓÊÏä£ÖйúµÚÒ»¾øÎÞÀ¬»øÓʼþɧÈų¬´óÓÊÏä
> 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
> >
> >
> >
> >
> >
> >
> >
> > ___________________________________________________________
> >
雅虎å…è´¹Gé‚��ï¼ä¸å›½ç�丢ãç»æ— 垃圾é‚�»¶éªšæ‰°è¶…大é‚��
> > http://cn.mail.yahoo.com
> >
> > _______________________________________________
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> --
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
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