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}. BoOn Tue, Feb 28, 2012 at 8:36 PM, <[email protected] <mailto:[email protected]>> wrote:Send gmx-users mailing list submissions to [email protected] <mailto:[email protected]> To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [email protected] <mailto:[email protected]> You can reach the person managing the list at [email protected] <mailto:[email protected]> When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." 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" <[email protected] <mailto:[email protected]>> Subject: Re: [gmx-users] change simulation temperature To: Discussion list for GROMACS users <[email protected] <mailto:[email protected]>> Message-ID: <[email protected] <mailto:[email protected]>> 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 <[email protected] <mailto:[email protected]>> Subject: Re: [gmx-users] change simulation temperature To: Discussion list for GROMACS users <[email protected] <mailto:[email protected]>> Message-ID: <[email protected] <mailto:[email protected]>> Content-Type: text/plain; charset="us-ascii" On 29/02/12, "bo.shuang" <[email protected] <mailto:[email protected]>> 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120229/c93c41c8/attachment-0001.html ------------------------------ Message: 3 Date: Tue, 28 Feb 2012 18:19:16 -0800 (PST) From: Adam Jion <[email protected] <mailto:[email protected]>> Subject: [gmx-users] NaN error using mdrun-gpu To: "[email protected] <mailto:[email protected]>" <[email protected] <mailto:[email protected]>> Message-ID: <[email protected] <mailto:[email protected]>> 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 -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120228/3c8c714f/attachment-0001.html ------------------------------ Message: 4 Date: Tue, 28 Feb 2012 18:34:56 -0800 (PST) From: Adam Jion <[email protected] <mailto:[email protected]>> Subject: [gmx-users] NaN error for mdrun-gpu To: "[email protected] <mailto:[email protected]>" <[email protected] <mailto:[email protected]>> Message-ID: <[email protected] <mailto:[email protected]>> 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 -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120228/8e3d8e95/attachment.html ------------------------------ -- gmx-users mailing list [email protected] <mailto:[email protected]> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 94, Issue 185 ******************************************
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