[gmx-users] Re: gmx-users Digest, Vol 94, Issue 185
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Feb 29 09:55:15 CET 2012
On 29/02/2012 4:24 PM, bo.shuang wrote:
> When I use explicit solvent, and set tau_t=2, it looks OK. The ions
> move faster when I increase the temperature. But when I use implicit
> solvent, it seems not change at all. Also, I am using sd instead of
> bd. I forgot to change it back. And in my understanding, the diffusive
> constant of Brown motion should be linear dependent on temperature, as
> shown below. Thank you!
Well if you're mangling your .mdp files then you might have used the
wrong one when you made your observation. Do check out manual 7.3.3 and
try again.
Mark
>
> \frac{\overline{x^2}}{2t}=D=\mu k_BT=\frac{\mu
> RT}{N}=\frac{RT}{6\pi\eta rN}.
>
>
>
> Bo
>
> On Tue, Feb 28, 2012 at 8:36 PM, <gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>> wrote:
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> Today's Topics:
>
> 1. Re: change simulation temperature (Justin A. Lemkul)
> 2. Re: change simulation temperature (Mark Abraham)
> 3. NaN error using mdrun-gpu (Adam Jion)
> 4. NaN error for mdrun-gpu (Adam Jion)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 28 Feb 2012 20:47:22 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> Subject: Re: [gmx-users] change simulation temperature
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4F4D83AA.3010502 at vt.edu <mailto:4F4D83AA.3010502 at vt.edu>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> bo.shuang wrote:
> > Hi, all,
> >
> > I have a question about change the temperature in simulation. When I
> > change the ref_t and gen_temp only, (from 300 to 400) I cannot
> see any
> > difference. I am thinking if I need to change tau_t also, since
> > diffusivity constant is also related to temperature. Am I right?
> >
>
> You're using a bd integrator, so the relationships here are not as
> straightforward as with md or sd integrators. I'm not experienced
> enough to
> comment on the implications of various settings for bd, but I
> would refer you to
> the manual, where the relationships are described (and how some of
> the .mdp
> keywords are used in special ways).
>
> Generally speaking, if you want to conduct a simulation at a different
> temperature, changing gen_temp and ref_t are indeed all that are
> required. The
> value of tau_t controls how tight the coupling is, nothing more.
>
> -Justin
>
> > Here is my mdp file:
> > title = OPLS Lysozyme NVT equilibration
> > ;define = -DPOSRES ; position restrain the protein
> > ; Run parameters
> > integrator = bd ; leap-frog integrator
> > nsteps = 500000 ; 2 * 500000 = 1000 ps
> > dt = 0.002 ; 2 fs
> > ; Output control
> > nstxout = 100 ; save coordinates every 0.2 ps
> > nstvout = 100 ; save velocities every 0.2 ps
> > nstenergy = 100 ; save energies every 0.2 ps
> > nstlog = 100 ; update log file every 0.2 ps
> > ; Bond parameters
> > continuation = yes ; first dynamics run
> > constraint_algorithm = lincs ; holonomic constraints
> > constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> > constrained
> > lincs_iter = 1 ; accuracy of LINCS
> > lincs_order = 4 ; also related to accuracy
> > ; Neighborsearching
> > ns_type = grid ; search neighboring grid cells
> > nstlist = 5 ; 10 fs
> > rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> > rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
> > rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
> > ; Electrostatics
> > coulombtype = PME ; Particle Mesh Ewald for long-range
> > electrostatics
> > pme_order = 4 ; cubic interpolation
> > fourierspacing = 0.16 ; grid spacing for FFT
> > ; Temperature coupling is on
> > tcoupl = V-rescale ; modified Berendsen thermostat
> > tc-grps = system ; two coupling groups - more accurate
> > tau_t = 0.01 ; time constant, in ps
> > ref_t = 400 ; reference temperature, one for each
> group,
> > in K
> > ; Pressure coupling is off
> > pcoupl = no ; no pressure coupling in NVT
> > ; Periodic boundary conditions
> > pbc = xyz ; 3-D PBC
> > ; Dispersion correction
> > DispCorr = EnerPres ; account for cut-off vdW scheme
> > ; Velocity generation
> > gen_vel = yes ; assign velocities from Maxwell
> > distribution changed
> > gen_temp = 400 ; temperature for Maxwell distribution
> > gen_seed = 100 ; generate a random seed
> > ld_seed=-1
> >
> >
> > Thank you!
> >
> > Bo
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 29 Feb 2012 12:48:05 +1100
> From: Mark Abraham <mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>>
> Subject: Re: [gmx-users] change simulation temperature
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <769090a715160.4f4e1e85 at anu.edu.au
> <mailto:769090a715160.4f4e1e85 at anu.edu.au>>
> Content-Type: text/plain; charset="us-ascii"
>
>
>
> On 29/02/12, "bo.shuang" <bs16 at rice.edu <mailto:bs16 at rice.edu>> wrote:
>
> > Hi, all,
> >
> > I have a question about change the temperature in simulation.
> When I change the ref_t and gen_temp only, (from 300 to 400) I
> cannot see any difference. I am thinking if I need to change tau_t
> also, since diffusivity constant is also related to temperature.
> Am I right?
> >
> > Here is my mdp file:
> > title = OPLS Lysozyme NVT equilibration
> > ;define = -DPOSRES ; position restrain the protein
> > ; Run parameters
> > integrator = bd ; leap-frog integrator
>
>
> By their nature, Browning and stochastic dynamics do not work with
> temperature coupling algorithms. IIRC gen_temp + gen_vel should
> have an effect on the initial conditions.
>
> Mark
>
>
> >
> >
> > nsteps = 500000 ; 2 * 500000 = 1000 ps
> > dt = 0.002 ; 2 fs
> > ; Output control
> > nstxout = 100 ; save coordinates every 0.2 ps
> > nstvout = 100 ; save velocities every 0.2 ps
> > nstenergy = 100 ; save energies every 0.2 ps
> > nstlog = 100 ; update log file every 0.2 ps
> > ; Bond parameters
> > continuation = yes ; first dynamics run
> > constraint_algorithm = lincs ; holonomic constraints
> > constraints = all-bonds ; all bonds (even heavy atom-H
> bonds) constrained
> > lincs_iter = 1 ; accuracy of LINCS
> > lincs_order = 4 ; also related to accuracy
> > ; Neighborsearching
> > ns_type = grid ; search neighboring grid cells
> > nstlist = 5 ; 10 fs
> > rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> > rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
> > rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
> > ; Electrostatics
> > coulombtype = PME ; Particle Mesh Ewald for long-range
> electrostatics
> > pme_order = 4 ; cubic interpolation
> > fourierspacing = 0.16 ; grid spacing for FFT
> > ; Temperature coupling is on
> > tcoupl = V-rescale ; modified Berendsen thermostat
> > tc-grps = system ; two coupling groups - more accurate
> > tau_t = 0.01 ; time constant, in ps
> > ref_t = 400 ; reference temperature, one for each
> group, in K
> > ; Pressure coupling is off
> > pcoupl = no ; no pressure coupling in NVT
> > ; Periodic boundary conditions
> > pbc = xyz ; 3-D PBC
> > ; Dispersion correction
> > DispCorr = EnerPres ; account for cut-off vdW scheme
> > ; Velocity generation
> > gen_vel = yes ; assign velocities from Maxwell
> distribution changed
> > gen_temp = 400 ; temperature for Maxwell distribution
> > gen_seed = 100 ; generate a random seed
> > ld_seed=-1
> >
> >
> > Thank you!
> >
> > Bo
> >
> >
>
>
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>
> Message: 3
> Date: Tue, 28 Feb 2012 18:19:16 -0800 (PST)
> From: Adam Jion <adamjion at yahoo.com <mailto:adamjion at yahoo.com>>
> Subject: [gmx-users] NaN error using mdrun-gpu
> To: "gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>"
> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> Message-ID:
> <1330481956.42489.YahooMailNeo at web30606.mail.mud.yahoo.com
> <mailto:1330481956.42489.YahooMailNeo at web30606.mail.mud.yahoo.com>>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi!
>
> I have a Palit 3GB GTX 580 GPU card to simulate about ~ 140 000 atoms.
> However, after an mdrun-gpu simulation of 5000 timesteps (each
> time step = 0.002), the log file starts to show NaN in the energy
> values.
>
> How do I fix this?
>
> Regards,
> Adam
>
> ps. The same system runs well in a conventional CPU-based mdrun.
> So I don't think its due to the system blowing up.
> pps. The GPU card reaches a temperature of ~ 88 degrees celsius
> after 5 minutes of simulation. Could this be the problem? However,
> I have another GPU card (MSI 1.5GB GTX 580) that works well with a
> smaller system (100 000 atoms) even at 85 degrees celsius.
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> ------------------------------
>
> Message: 4
> Date: Tue, 28 Feb 2012 18:34:56 -0800 (PST)
> From: Adam Jion <adamjion at yahoo.com <mailto:adamjion at yahoo.com>>
> Subject: [gmx-users] NaN error for mdrun-gpu
> To: "gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>"
> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> Message-ID:
> <1330482896.34758.YahooMailNeo at web30608.mail.mud.yahoo.com
> <mailto:1330482896.34758.YahooMailNeo at web30608.mail.mud.yahoo.com>>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi!
>
> I have a Palit 3GB GTX 580 GPU card to simulate about ~ 140 000 atoms.
> However, after an mdrun-gpu simulation of 5000 timesteps (each
> time step = 0.002), the log file starts to show NaN in the energy
> values.
>
> How do I fix this?
>
> Regards,
> Adam
>
> ps. The same system runs well in a conventional CPU-based mdrun.
> So I don't think its due to the system blowing up.
> pps. The GPU card reaches a temperature of ~ 88 degrees celsius
> after 5 minutes of simulation. Could this be the problem? However,
> I have another GPU card (MSI 1.5GB GTX 580) that works well with a
> smaller system (100 000 atoms) even at 85 degrees celsius.
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> End of gmx-users Digest, Vol 94, Issue 185
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