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!<br>
<br><dl><dd><img class="tex" alt="\frac{\overline{x^2}}{2t}=D=\mu k_BT=\frac{\mu RT}{N}=\frac{RT}{6\pi\eta rN}." src="http://upload.wikimedia.org/wikipedia/en/math/3/1/2/3122902a8274ad854726c177994d798a.png"></dd></dl><br>
<br>Bo<br><br><div class="gmail_quote">On Tue, Feb 28, 2012 at 8:36 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Today's Topics:<br>
<br>
1. Re: change simulation temperature (Justin A. Lemkul)<br>
2. Re: change simulation temperature (Mark Abraham)<br>
3. NaN error using mdrun-gpu (Adam Jion)<br>
4. NaN error for mdrun-gpu (Adam Jion)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 28 Feb 2012 20:47:22 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] change simulation temperature<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4F4D83AA.3010502@vt.edu">4F4D83AA.3010502@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
bo.shuang wrote:<br>
> Hi, all,<br>
><br>
> I have a question about change the temperature in simulation. When I<br>
> change the ref_t and gen_temp only, (from 300 to 400) I cannot see any<br>
> difference. I am thinking if I need to change tau_t also, since<br>
> diffusivity constant is also related to temperature. Am I right?<br>
><br>
<br>
You're using a bd integrator, so the relationships here are not as<br>
straightforward as with md or sd integrators. I'm not experienced enough to<br>
comment on the implications of various settings for bd, but I would refer you to<br>
the manual, where the relationships are described (and how some of the .mdp<br>
keywords are used in special ways).<br>
<br>
Generally speaking, if you want to conduct a simulation at a different<br>
temperature, changing gen_temp and ref_t are indeed all that are required. The<br>
value of tau_t controls how tight the coupling is, nothing more.<br>
<br>
-Justin<br>
<br>
> Here is my mdp file:<br>
> title = OPLS Lysozyme NVT equilibration<br>
> ;define = -DPOSRES ; position restrain the protein<br>
> ; Run parameters<br>
> integrator = bd ; leap-frog integrator<br>
> nsteps = 500000 ; 2 * 500000 = 1000 ps<br>
> dt = 0.002 ; 2 fs<br>
> ; Output control<br>
> nstxout = 100 ; save coordinates every 0.2 ps<br>
> nstvout = 100 ; save velocities every 0.2 ps<br>
> nstenergy = 100 ; save energies every 0.2 ps<br>
> nstlog = 100 ; update log file every 0.2 ps<br>
> ; Bond parameters<br>
> continuation = yes ; first dynamics run<br>
> constraint_algorithm = lincs ; holonomic constraints<br>
> constraints = all-bonds ; all bonds (even heavy atom-H bonds)<br>
> constrained<br>
> lincs_iter = 1 ; accuracy of LINCS<br>
> lincs_order = 4 ; also related to accuracy<br>
> ; Neighborsearching<br>
> ns_type = grid ; search neighboring grid cells<br>
> nstlist = 5 ; 10 fs<br>
> rlist = 1.0 ; short-range neighborlist cutoff (in nm)<br>
> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)<br>
> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)<br>
> ; Electrostatics<br>
> coulombtype = PME ; Particle Mesh Ewald for long-range<br>
> electrostatics<br>
> pme_order = 4 ; cubic interpolation<br>
> fourierspacing = 0.16 ; grid spacing for FFT<br>
> ; Temperature coupling is on<br>
> tcoupl = V-rescale ; modified Berendsen thermostat<br>
> tc-grps = system ; two coupling groups - more accurate<br>
> tau_t = 0.01 ; time constant, in ps<br>
> ref_t = 400 ; reference temperature, one for each group,<br>
> in K<br>
> ; Pressure coupling is off<br>
> pcoupl = no ; no pressure coupling in NVT<br>
> ; Periodic boundary conditions<br>
> pbc = xyz ; 3-D PBC<br>
> ; Dispersion correction<br>
> DispCorr = EnerPres ; account for cut-off vdW scheme<br>
> ; Velocity generation<br>
> gen_vel = yes ; assign velocities from Maxwell<br>
> distribution changed<br>
> gen_temp = 400 ; temperature for Maxwell distribution<br>
> gen_seed = 100 ; generate a random seed<br>
> ld_seed=-1<br>
><br>
><br>
> Thank you!<br>
><br>
> Bo<br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Wed, 29 Feb 2012 12:48:05 +1100<br>
From: Mark Abraham <<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] change simulation temperature<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:769090a715160.4f4e1e85@anu.edu.au">769090a715160.4f4e1e85@anu.edu.au</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
<br>
<br>
On 29/02/12, "bo.shuang" <<a href="mailto:bs16@rice.edu">bs16@rice.edu</a>> wrote:<br>
<br>
> Hi, all,<br>
><br>
> 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?<br>
><br>
> Here is my mdp file:<br>
> title = OPLS Lysozyme NVT equilibration<br>
> ;define = -DPOSRES ; position restrain the protein<br>
> ; Run parameters<br>
> integrator = bd ; leap-frog integrator<br>
<br>
<br>
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.<br>
<br>
Mark<br>
<br>
<br>
><br>
><br>
> nsteps = 500000 ; 2 * 500000 = 1000 ps<br>
> dt = 0.002 ; 2 fs<br>
> ; Output control<br>
> nstxout = 100 ; save coordinates every 0.2 ps<br>
> nstvout = 100 ; save velocities every 0.2 ps<br>
> nstenergy = 100 ; save energies every 0.2 ps<br>
> nstlog = 100 ; update log file every 0.2 ps<br>
> ; Bond parameters<br>
> continuation = yes ; first dynamics run<br>
> constraint_algorithm = lincs ; holonomic constraints<br>
> constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained<br>
> lincs_iter = 1 ; accuracy of LINCS<br>
> lincs_order = 4 ; also related to accuracy<br>
> ; Neighborsearching<br>
> ns_type = grid ; search neighboring grid cells<br>
> nstlist = 5 ; 10 fs<br>
> rlist = 1.0 ; short-range neighborlist cutoff (in nm)<br>
> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)<br>
> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)<br>
> ; Electrostatics<br>
> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics<br>
> pme_order = 4 ; cubic interpolation<br>
> fourierspacing = 0.16 ; grid spacing for FFT<br>
> ; Temperature coupling is on<br>
> tcoupl = V-rescale ; modified Berendsen thermostat<br>
> tc-grps = system ; two coupling groups - more accurate<br>
> tau_t = 0.01 ; time constant, in ps<br>
> ref_t = 400 ; reference temperature, one for each group, in K<br>
> ; Pressure coupling is off<br>
> pcoupl = no ; no pressure coupling in NVT<br>
> ; Periodic boundary conditions<br>
> pbc = xyz ; 3-D PBC<br>
> ; Dispersion correction<br>
> DispCorr = EnerPres ; account for cut-off vdW scheme<br>
> ; Velocity generation<br>
> gen_vel = yes ; assign velocities from Maxwell distribution changed<br>
> gen_temp = 400 ; temperature for Maxwell distribution<br>
> gen_seed = 100 ; generate a random seed<br>
> ld_seed=-1<br>
><br>
><br>
> Thank you!<br>
><br>
> Bo<br>
><br>
><br>
<br>
<br>
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Message: 3<br>
Date: Tue, 28 Feb 2012 18:19:16 -0800 (PST)<br>
From: Adam Jion <<a href="mailto:adamjion@yahoo.com">adamjion@yahoo.com</a>><br>
Subject: [gmx-users] NaN error using mdrun-gpu<br>
To: "<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:1330481956.42489.YahooMailNeo@web30606.mail.mud.yahoo.com">1330481956.42489.YahooMailNeo@web30606.mail.mud.yahoo.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi!<br>
<br>
I have a Palit 3GB GTX 580 GPU card to simulate about ~ 140 000 atoms.<br>
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.<br>
<br>
How do I fix this?<br>
<br>
Regards,<br>
Adam<br>
<br>
ps. The same system runs well in a conventional CPU-based mdrun. So I don't think its due to the system blowing up.<br>
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.<br>
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<br>
Message: 4<br>
Date: Tue, 28 Feb 2012 18:34:56 -0800 (PST)<br>
From: Adam Jion <<a href="mailto:adamjion@yahoo.com">adamjion@yahoo.com</a>><br>
Subject: [gmx-users] NaN error for mdrun-gpu<br>
To: "<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:1330482896.34758.YahooMailNeo@web30608.mail.mud.yahoo.com">1330482896.34758.YahooMailNeo@web30608.mail.mud.yahoo.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi!<br>
<br>
I have a Palit 3GB GTX 580 GPU card to simulate about ~ 140 000 atoms.<br>
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.<br>
<br>
How do I fix this?<br>
<br>
Regards,<br>
Adam<br>
<br>
ps. The same system runs well in a conventional CPU-based mdrun. So I don't think its due to the system blowing up.<br>
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.<br>
-------------- next part --------------<br>
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End of gmx-users Digest, Vol 94, Issue 185<br>
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