Dear Berk, 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.
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. ++++++++++++++++++++++++++++++++++++ title = SS2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 1000000 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 0 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 rvdw_switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 283.0 0.0 gen_vel = yes gen_temp = 283.0 gen_seed = 181726 freezegrps = Tmp2 freezedim = Y Y Y ++++++++++++++++++++++++++++++++++++ Thanks very much Srinivas. On Wed, Apr 21, 2010 at 10:53 AM, Berk Hess <g...@hotmail.com> wrote: > Hi, > > I moved this to the user list, so it will be of use to others. > > I have no clue what you are trying to do, what groups you are accelerating > or freezing. > So we can't help you without further information. > Setting up simulations with frozen groups, accelerate groups or different > coupling > temperatures is tricky and will in most cases destroy energy conservation. > > Berk > > ------------------------------ > Date: Wed, 21 Apr 2010 10:41:25 -0400 > Subject: Fwd: [Bug 404] energy increase in nvt and nve simiulations > From: jampa...@gmail.com > To: g...@hotmail.com > > > Dear Berk, > > Thanks for the reply, based on the suggestions of Justin from Mailing list > i have tried the simulation in the following way. > > 1. I have removed the "acc_grps" option > 2. I have used "energygrp_excl" to avoid interaction between non > frozen-frozen and frozen-frozen. > > Still i have seen some velocity to the frozen atoms (i have printed > velocities from trajectory) and drift in the energy. > > 3. I also switched of PBC and used "coulombtype = different options here" > In this case i observed that some of the water molecules try to escape from > the system. > > > But i am not clear about center of mass motion. Should i allow to change > center of mass with "comm_mode = No" option? > > Could you please let me know if you want more details about this? I am > still struggling with running this simulation. > > Thanks for your kind help > Srinivas. > > > -- > ********************************************* > J. Srinivasa Rao > Post-doctoral Research Associate > C/o Prof. Luis R Cruz Cruz > Computational Biophysics Group > Department of Physics > Drexel University > 3141 Chestnut St > Philadelphia, PA 19104, USA. > Ph: Off: 215-895-1989 > Mob: 704-706-4191 > Web:http://jsrao.web.officelive.com/default.aspx > ********************************************** > > > > ------------------------------ > New Windows 7: Find the right PC for you. Learn > more.<http://windows.microsoft.com/shop> > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ********************************************* J. Srinivasa Rao Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx **********************************************
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