Dear Berk,<div><br></div><div>I am sorry for poor communication, Herewith i am giving my md.mdp file. I this file as you could see i am using two temp coupling groups Tmp1 is protein and a 2nm spherical layer of water around it, and the second one Tmp2 which has only water. Now i want to fix the Tmp2 and apply 0 K to it. As you could see that from the file below i have taken Tcoupl = V-rescale and two coupling groups Tmp1 and Tmp2 to make a frozen wall. I am not accelerating any group here.</div>
<div><br></div><div>In other words the goal of simulation is to check the behavior of protein is a confined sphere, i am trying to make frozen wall by freezing water around the protein after a specified distance. </div><meta http-equiv="content-type" content="text/html; charset=utf-8"><div>
<br></div><div><br></div><div>++++++++++++++++++++++++++++++++++++</div><div><div>title = SS2130</div><div>cpp = /usr/bin/cpp</div><div>constraints = all-bonds</div><div>integrator = md</div>
<div>dt = 0.002 ; ps !</div><div>nsteps = 1000000 </div><div>nstxout = 1000</div><div>nstvout = 1000</div><div>nstfout = 0</div><div>nstlog = 0</div><div>nstenergy = 1000</div>
<div>nstlist = 5</div><div>ns_type = grid</div><div>rlist = 1.0</div><div>coulombtype = PME</div><div>rcoulomb = 1.0</div><div>rvdw = 1.0</div><div>rvdw_switch = 0.9</div>
<div>fourierspacing = 0.12</div><div>fourier_nx = 0</div><div>fourier_ny = 0</div><div>fourier_nz = 0</div><div>pme_order = 4</div><div>ewald_rtol = 1e-5</div><div>optimize_fft = yes</div><div>
Tcoupl = V-rescale</div><div>tau_t = 0.1 0.1</div><div>tc-grps = Tmp1 Tmp2</div><div>ref_t = 283.0 0.0</div><div>gen_vel = yes</div><div>gen_temp = 283.0</div>
<div>gen_seed = 181726</div><div>freezegrps = Tmp2</div><div>freezedim = Y Y Y</div></div><div>++++++++++++++++++++++++++++++++++++</div><div><br></div><div><br></div><div>Thanks very much</div><div>Srinivas.<br>
<div class="gmail_quote">On Wed, Apr 21, 2010 at 10:53 AM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div>
Hi,<br><br>I moved this to the user list, so it will be of use to others.<br><br>I have no clue what you are trying to do, what groups you are accelerating or freezing.<br>So we can't help you without further information.<br>
Setting up simulations with frozen groups, accelerate groups or different coupling<br>temperatures is tricky and will in most cases destroy energy conservation.<br><br>Berk<br><br><hr>Date: Wed, 21 Apr 2010 10:41:25 -0400<br>
Subject: Fwd: [Bug 404] energy increase in nvt and nve simiulations<br>From: <a href="mailto:jampanis@gmail.com" target="_blank">jampanis@gmail.com</a><br>To: <a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a><div>
<div></div><div class="h5"><br><br>Dear Berk,<br><br>Thanks for the reply, based on the suggestions of Justin from
Mailing list i have tried the simulation in the following way.<br><br>1.
I have removed the<a name="12820dd117ae2dca_12820cca65690a12_neq"> "acc_grps"</a> option<br>2.
I have used<a name="12820dd117ae2dca_12820cca65690a12_egexcl"> "energygrp_excl" to avoid
interaction between non frozen-frozen and frozen-frozen.<br>
<br>Still i have seen some velocity to the frozen atoms (i have printed
velocities from trajectory) and drift in the energy.<br><br>3. I also
switched of PBC and used</a><a name="12820dd117ae2dca_12820cca65690a12_el"> "coulombtype</a><a name="12820dd117ae2dca_12820cca65690a12_egexcl"> = different options here" In this case
i observed that some of the water molecules try to escape from the
system.<br>
<br><br>But i am not clear about center of mass motion. Should i allow
to change center of mass with</a> "comm_mode<a name="12820dd117ae2dca_12820cca65690a12_egexcl"> = No" option?<br><br>Could you please
let me know if you want more details about this? I am still struggling
with running this simulation.<br>
<br>Thanks for your kind help<br>Srinivas.</a><br><br clear="all"><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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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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