[gmx-users] Re: gmx-users Digest, Vol 94, Issue 185
bo.shuang
bs16 at rice.edu
Wed Feb 29 06:24:08 CET 2012
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!
[image: \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> wrote:
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> Today's Topics:
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> 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>
> Subject: Re: [gmx-users] change simulation temperature
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <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 | (540) 231-9080
> 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>
> Subject: Re: [gmx-users] change simulation temperature
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <769090a715160.4f4e1e85 at anu.edu.au>
> Content-Type: text/plain; charset="us-ascii"
>
>
>
> On 29/02/12, "bo.shuang" <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>
> Subject: [gmx-users] NaN error using mdrun-gpu
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID:
> <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>
> Subject: [gmx-users] NaN error for mdrun-gpu
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID:
> <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.
> -------------- next part --------------
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> End of gmx-users Digest, Vol 94, Issue 185
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