Hi Tanping Li,<br><br>What this tells you is that you're independently coupling your sodium ions to the heat bath, which makes their temperature fluctuate like crazy and may introduce artefacts. Couple the sodium ions together with the solvent. This has been dealt with on the user list several times, check the archives. Also, it's a bit dubious to talk about the temperature of a single residue... Temperature is a collective property. Don't start to seperately couple a single residue. It's ok like that.
<br><br>Cheers,<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 11/1/05, <b class="gmail_sendername">Tanping Li</b> <<a href="mailto:jia_11_osu@yahoo.com">jia_11_osu@yahoo.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Devid,<br><br>Under pme and globlly T-coupling at 295K, I get the<br>tem for protein, water and Na in my system like this:<br><br> Protein Sol Na<br>Average 293 297 434<br><br>Is it acceptable?
<br><br><br>The tem of Na is very large. Does that tells me that<br>thfe charged groups in protein will also deviate far<br>away fro the average Tem? I am analysising the<br>interaction between a specific residue and close
<br>waters. Do I need to seperately couple their tem since<br>I find out that tem of this specific residue(trp) is a<br>little bit from 295K. Thank you very much for your<br>help.<br><br><br>Tanping<br><br><br><br>--- David <
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br><br>> On Tue, 2005-11-01 at 08:10 -0800, Tanping Li wrote:<br>> > Devid,<br>> ><br>> > Thank you very much for your reply. I used globlly
<br>> > T-coupling and pme. Now I am nervous about it.<br>> > Firstly, I want to check the temprature of protein<br>> and<br>> > Sol seperately. Is there any way in Gromacs to get<br>> the<br>> > Tem of specific group, instead of calculating Tem
<br>> by<br>> > the velocity by myself?<br>> ><br>><br>> g_traj<br>><br>> ><br>> > Tanping<br>> ><br>> > --- David <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a>> wrote:<br>> ><br>> > > On Tue, 2005-11-01 at 08:16 +0100, Erik Lindahl<br>> > > wrote:<br>> > > > Hi,<br>> > > ><br>> > > > If you use PME you're fine with either. If you
<br>> > > have cut-offs and<br>> > > > large drifts in energy you run a risk of e.g.<br>> the<br>> > > water beeing cooler<br>> > > > than the protein if you only use global<br>
> coupling.<br>> > ><br>> > > I'm not sure this is correct. Heat exchange<br>> between<br>> > > components for which<br>> > > the forces are relatively weak is as far as I<br>> know a
<br>> > > problem. Please<br>> > > test it and report back to the list. It may also<br>> be<br>> > > slightly worse for<br>> > > GROMOS than for OPLS since OPLS has more charged<br>> > > atoms in the protein
<br>> > > than GROMOS.<br>> > ><br>> > > Why don't you do four 500 ps sims with GROMOS<br>> and<br>> > > OPLS and with separate<br>> > > coupling groups and only one, and make a table
<br>> of<br>> > > the protein<br>> > > temperatures in respective simulations. You will<br>> > > have to save velocities<br>> > > relatively often to compute the temperature in<br>> the
<br>> > > simulation where you<br>> > > only have one group.<br>> > ><br>> > > ><br>> > > > Cheers,<br>> > > ><br>> > > > Erik<br>> > > >
<br>> > > ><br>> > > > On Nov 1, 2005, at 1:28 AM, Tanping Li wrote:<br>> > > ><br>> > > > > Dear all,<br>> > > > ><br>> > > > > I am simulating the hyrdation issume of
<br>> protein<br>> > > under<br>> > > > > NVT condition. We use Gromos96 force field.<br>> I<br>> > > noticed<br>> > > > > that in the tutorial mdp file, the protein<br>
> and<br>> > > solvent<br>> > > > > are tem coupled seperately. Could I use the<br>> > > global<br>> > > > > tem-coupling? Is there any real difference<br>> > > between
<br>> > > > > them?<br>> > > > > Thank you very much for your reply.<br>> > > > ><br>> > > > ><br>> > > > > Best<br>> > > > > Tanping Li
<br>> > > > ><br>> _______________________________________________<br>> > > > > gmx-users mailing list<br>> > > > > <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
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<br>> > > > ><br>> > > ><br>> > > ><br>> > ><br>> ><br>><br>-----------------------------------------------------------<br>> > > > Erik Lindahl <<a href="mailto:lindahl@sbc.su.se">
lindahl@sbc.su.se</a>><br>> > > > Assistant Professor, Stockholm Bioinformatics<br>> > > Center<br>> > > > Stockholm University, SE 106 91 Stockholm<br>> > > > Phone: +46 8 5537 8564 Fax: +46 8 5537
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<br>> Biophysics group,<br>> Dept. of Cell and Molecular Biology, Uppsala<br>> University.<br>> Husargatan 3, Box 596, 75124 Uppsala,<br>> Sweden<br>> phone: 46 18 471 4205 fax: 46 18 511 755
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<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>