<div>Dear Justin,</div>
<div> </div>
<div>Thanks for your responce. Here is my mdp file. </div>
<div> </div>
<div>+++++++++++++++++++++++++++++++++++++++</div>
<div>title = AB2130<br>cpp = /usr/bin/cpp<br>constraints = all-bonds<br>integrator = md<br>dt = 0.004 ; ps !<br>nsteps = 25000000 ; total 100.0 ns.<br>nstcomm = 1<br>
nstxout = 1000 ; collect data every 2.0 ps<br>nstvout = 1000 ; collect velocity every 2.0 ps<br>nstfout = 0<br>nstlog = 0<br>nstenergy = 1000 ; collect energy every 2.0 ps<br>nstlist = 10<br>
ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>rvdw = 1.0<br>rvdw_switch = 0.9<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>
fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = V-rescale<br>tau_t = 0.1 0.1<br>tc-grps = Tmp1 Tmp2<br>
ref_t = 283.0 0.0<br>gen_vel = yes<br>gen_temp = 283.0<br>acc_grps = Tmp1<br>accelerate = 0.1 0.1 0.1<br>gen_seed = 181726<br>freezegrps = Tmp2<br>freezedim = Y Y Y</div>
<div>++++++++++++++++++++++++++++++++++++++++++++++++<br></div>
<div>Thanks</div>
<div>Srinivas.<br></div>
<div class="gmail_quote">On Thu, Apr 8, 2010 at 7:52 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im"><br><br>jampani srinivas wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Hi<br> Thanks for your response, I am allowing the two groups (frozen and non-frozen) groups interact each other, i guess i am getting the energy of total system from g_energy.<br>
I checked the velocities of frozen group atoms, they are not "zero". I have seen in git master that this problem was fixed and updated in md.c file, I have downloaded this from git master and compiled my gromacs again still i found that frozen atoms gets the initial velocity.<br>
I am not at all clear why the energy of system should blow up, can you please help me if there is solution for this.<br> <br></blockquote><br></div>I haven't been following this closely; can you post an .mdp file?<br>
<br>-Justin<br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Thanks in advance.<br> Srinivas.
<div class="im"><br><br>On Wed, Apr 7, 2010 at 4:47 PM, ms <<a href="mailto:devicerandom@gmail.com" target="_blank">devicerandom@gmail.com</a> <mailto:<a href="mailto:devicerandom@gmail.com" target="_blank">devicerandom@gmail.com</a>>> wrote:<br>
<br> jampani srinivas ha scritto:<br> > Dear Berk,<br> ><br> > I am sorry if i am confusing you with my poor description of problem,<br> > actually I have submitted simulation with two temperature<br>
coupling groups (i<br> > think you already know that from our earlier conversations) and<br> found that<br> > there is a continuous increase in the total energy of the system.<br> I could<br> > not observe any blowing in the output file but the system energy is<br>
> continuously increasing, i am using 4fs time step here. Can you<br> please let<br> > me know if i have to give more details?<br> ><br><br> Which part of the system is increasing its energy?<br><br>
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J. Srinivasa Rao<br>Post-doctoral Research Associate<br>C/o Prof. Luis R Cruz Cruz<br>Computational Biophysics Group<br>Department of Physics<br>Drexel University<br>3141 Chestnut St<br>Philadelphia, PA 19104, USA.<br>Ph: Off: 215-895-1989<br>
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<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> | (540) 231-9080<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><font color="#888888">-- <br>
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J. Srinivasa Rao <br>Post-doctoral Research Associate<br>C/o Prof. Luis R Cruz Cruz<br>Computational Biophysics Group<br>Department of Physics<br>Drexel University<br>3141 Chestnut St<br>Philadelphia, PA 19104, USA.<br>Ph: Off: 215-895-1989<br>
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