[gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations
jampani srinivas
jampanis at gmail.com
Thu Apr 22 12:47:42 CEST 2010
Dear Berk,
I have run it for 5ns, as you said for first 1ns i have not seen much drift
in the energy there after energy is slowly increasing in each step. Should i
run it again and send you the edr file? can you please let me know on which
version of gromacs you have run this file?
Thanks very much
Srinivas.
On Thu, Apr 22, 2010 at 3:25 AM, Berk Hess <gmx3 at hotmail.com> wrote:
> Hi,
>
> I quickly ran the tpr file you provided on bugzilla, but I don't see an
> enormous energy drift.
> What do you mean with "the energy explodes"?
>
> Berk
>
> ------------------------------
> Date: Wed, 21 Apr 2010 11:18:53 -0400
> Subject: Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve
> simiulations
> From: jampanis at gmail.com
> To: gmx-users at gromacs.org
>
>
> 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 <gmx3 at 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: jampanis at gmail.com
> To: gmx3 at 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
> **********************************************
>
>
>
> ------------------------------
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> --
> *********************************************
> 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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*********************************************
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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