<div>Dear Justin,</div>
<div> </div>
<div>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal">I am sorry for the poor description of the problem, OK let me explain you clearly here.</p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal"> </p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal">I have taken a decapeptide and solvated it with box size 6.0 nm, I want to create a frozen wall (confined sphere) around protein after a certain radius (in this case it is 2.5 nm). To achieve this i made two temperature coupling groups, first (Tmp1) one has protein and waters within 2.5nm from the center of the box and rest is second temperature coupling group (Tmp2). Initially when i run the simulation it was creating nrdf = 0 for both groups, Berk has helped me with a file readir.c file, i compiled my gromacs again that problem was solved. I have submitted simulations again and found that the energy was blowing up. I think you know the story after this. Earlier I want protein to interact with inner wall of the frozen group and check what happens, because of this I have never looked at the energygrps_excl option. I have done with both 2 and 4 fs time steps and I took 4fs option to speed up the simulation, and I have to still look at the paper you suggested me. </p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal"> </p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal">Thanks for your suggestions, I have implemented your suggestion one after the other, finally when i use the energygrps_excl option it worked out. Now there is no sudden drift in the energy, and also i checked the velocities of non-frozen group is mostly zero (except for first frame)</p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal"> </p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal">When I use the energygrps_excel option in the following way i am getting the below mentioned note i have to still understand what is this message. On the other hand if i use only "energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1" line in mdp file i am getting fatal error. Is it necessary to to define the energy groups first and later exclude the energy option? </p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal">+++++++++++++++++++++++++++++</p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal">energygrps = Tmp1 Tmp2<br>energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1</p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal">++++++++++++++++++++++++++++++++</p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal">NOTE</p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal">"Can not exclude the lattice Coulomb energy between energy groups" </p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal">I used -maxwarn option here and generated the tpr file. I hope this does not harm the simulation. </p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal"> </p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal">Please let me know your comments and suggestion.</p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal"> </p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal">Thanks very much for your kind help.</p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal"> </p>
<p style="TEXT-ALIGN: justify; MARGIN: 0in 0in 0pt" class="MsoNormal">Srinivas.</p><br><br></div>
<div class="gmail_quote">On Thu, Apr 8, 2010 at 8:21 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>
<div></div>
<div class="h5"><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">Dear Justin,<br> Thanks for your responce. Here is my mdp file.<br> +++++++++++++++++++++++++++++++++++++++<br>
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<br>
++++++++++++++++++++++++++++++++++++++++++++++++<br></blockquote><br></div></div>There are a whole host of reasons that you're seeing an energy drift. Perhaps you should give a more detailed description of what you're trying to do. Per your original message, you imply that you have a very simple system of some frozen and non-frozen group, which is clearly oversimplified. A few thoughts:<br>
<br>1. You're applying constant acceleration, so you're introducing non-equilibrium conditions. What is Tmp1? Could it be working against Tmp2 (frozen) in some way that is causing a clash?<br><br>2. You're not using energrygrp_excl for your frozen group. Per the manual:<br>
<br>"To avoid spurious contributions to the virial and pressure due to large forces between completely frozen atoms you need to use energy group exclusions, this also saves computing time."<br><br>3. Are you using virtual sites in addition to constraints? Does a shorter timestep alleviate the energy drift? Have a look at the Gromacs 4 paper for notes about use of virtual sites and constraints, and the effect on what's reasonable for the time step.<br>
<br>I'd suggest working through this systematically - you've got a ton of variables that could be opposing one another. Introduce them one at a time to see where your system starts to break down.<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<br>Srinivas.
<div class="im"><br>On Thu, Apr 8, 2010 at 7:52 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> jampani srinivas wrote:<br><br> Hi<br> Thanks for your response, I am allowing the two groups (frozen<br> and non-frozen) groups interact each other, i guess i am getting<br> the energy of total system from g_energy.<br>
I checked the velocities of frozen group atoms, they are not<br> "zero". I have seen in git master that this problem was fixed<br> and updated in md.c file, I have downloaded this from git master<br>
and compiled my gromacs again still i found that frozen atoms<br> gets the initial velocity.<br> I am not at all clear why the energy of system should blow up,<br> can you please help me if there is solution for this.<br>
<br><br> I haven't been following this closely; can you post an .mdp file?<br><br> -Justin<br><br> Thanks in advance.<br> Srinivas.<br><br><br> On Wed, Apr 7, 2010 at 4:47 PM, ms <<a href="mailto:devicerandom@gmail.com" target="_blank">devicerandom@gmail.com</a><br>
</div> <mailto:<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>
<div class="im"><br> <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<br> of problem,<br> > actually I have submitted simulation with two temperature<br> coupling groups (i<br> > think you already know that from our earlier<br>
conversations) and<br> found that<br> > there is a continuous increase in the total energy of the<br> system.<br> I could<br> > not observe any blowing in the output file but the system<br>
energy is<br> > continuously increasing, i am using 4fs time step here.<br> 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>
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<br><br><br><br> -- *********************************************<br> 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> Mob: 704-706-4191<br> Web:<a href="http://jsrao.web.officelive.com/default.aspx" target="_blank">http://jsrao.web.officelive.com/default.aspx</a><br>
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<div class="h5"><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>
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