[gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations

[jampani srinivas]

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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