<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 29/02/2012 4:24 PM, bo.shuang wrote:
<blockquote
cite="mid:CA+4uorPDHf3076Z5neo3OOqUc_O=_md8x6N+x80n8oD2E2bB=w@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CA+4uorPDHf3076Z5neo3OOqUc_O=_md8x6N+x80n8oD2E2bB=w@mail.gmail.com"
type="cite">
<br>
<dl>
<dd><img moz-do-not-send="true" 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 moz-do-not-send="true"
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">
Send gmx-users mailing list submissions to<br>
<a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>
<br>
You can reach the person managing the list at<br>
<a moz-do-not-send="true"
href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br>
<br>
When replying, please edit your Subject line so it is more
specific<br>
than "Re: Contents of gmx-users digest..."<br>
<br>
<br>
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 moz-do-not-send="true"
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
moz-do-not-send="true" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a moz-do-not-send="true"
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 moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | <a moz-do-not-send="true"
href="tel:%28540%29%20231-9080" value="+15402319080">(540)
231-9080</a><br>
<a moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a moz-do-not-send="true"
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 moz-do-not-send="true"
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>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20120229/c93c41c8/attachment-0001.html"
target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20120229/c93c41c8/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 28 Feb 2012 18:19:16 -0800 (PST)<br>
From: Adam Jion <<a moz-do-not-send="true"
href="mailto:adamjion@yahoo.com">adamjion@yahoo.com</a>><br>
Subject: [gmx-users] NaN error using mdrun-gpu<br>
To: "<a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>"
<<a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a moz-do-not-send="true"
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>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20120228/3c8c714f/attachment-0001.html"
target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20120228/3c8c714f/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Tue, 28 Feb 2012 18:34:56 -0800 (PST)<br>
From: Adam Jion <<a moz-do-not-send="true"
href="mailto:adamjion@yahoo.com">adamjion@yahoo.com</a>><br>
Subject: [gmx-users] NaN error for mdrun-gpu<br>
To: "<a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>"
<<a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a moz-do-not-send="true"
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>
An HTML attachment was scrubbed...<br>
URL: <a moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20120228/8e3d8e95/attachment.html"
target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20120228/8e3d8e95/attachment.html</a><br>
<br>
------------------------------<br>
<span class="HOEnZb"><font color="#888888"><br>
--<br>
gmx-users mailing list<br>
<a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
<br>
End of gmx-users Digest, Vol 94, Issue 185<br>
******************************************<br>
<br>
</font></span></blockquote>
</div>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>