[gmx-users] problem with total energy

[jampani srinivas]

Dear Justin,

Thanks for your responce. Here is my mdp file.

+++++++++++++++++++++++++++++++++++++++
title           = AB2130
cpp             = /usr/bin/cpp
constraints     = all-bonds
integrator      = md
dt              = 0.004 ; ps !
nsteps          = 25000000 ; total 100.0 ns.
nstcomm         = 1
nstxout         = 1000 ; collect data     every 2.0 ps
nstvout         = 1000 ; collect velocity every 2.0 ps
nstfout         = 0
nstlog          = 0
nstenergy       = 1000 ; collect energy   every 2.0 ps
nstlist         = 10
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
; Berendsen temperature coupling is on in two groups
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
acc_grps        = Tmp1
accelerate      = 0.1 0.1 0.1
gen_seed        = 181726
freezegrps      = Tmp2
freezedim       = Y Y Y
++++++++++++++++++++++++++++++++++++++++++++++++
Thanks
Srinivas.
On Thu, Apr 8, 2010 at 7:52 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> jampani srinivas wrote:
>
>> Hi
>>  Thanks for your response, I am allowing the two groups (frozen and
>> non-frozen) groups interact each other, i guess i am getting the energy of
>> total system from g_energy.
>>  I checked the velocities of frozen group atoms, they are not "zero". I
>> have seen in git master that this problem was fixed and updated in md.c
>> file, I have downloaded this from git master and compiled my gromacs again
>> still i found that frozen atoms gets the initial velocity.
>>  I am not at all clear why the energy of system should blow up, can you
>> please help me if there is solution for this.
>>
>>
>
> I haven't been following this closely; can you post an .mdp file?
>
> -Justin
>
> Thanks in advance.
>>  Srinivas.
>>
>>
>> On Wed, Apr 7, 2010 at 4:47 PM, ms <devicerandom at gmail.com <mailto:
>> devicerandom at gmail.com>> wrote:
>>
>>    jampani srinivas ha scritto:
>>     > Dear Berk,
>>     >
>>     > I am sorry if i am confusing you with my poor description of
>> problem,
>>     > actually I have submitted simulation with two temperature
>>    coupling groups (i
>>     > think you already know that from our earlier conversations) and
>>    found that
>>     > there is a continuous increase in the total energy of the system.
>>    I could
>>     > not observe any blowing in the output file but the system energy is
>>     > continuously increasing, i am using 4fs time step here. Can you
>>    please let
>>     > me know if i have to give more details?
>>     >
>>
>>    Which part of the system is increasing its energy?
>>
>>    m.
>>    --
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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
>> **********************************************
>>
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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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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