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

[jampani srinivas]

Dear Berk,

First of all thanks very much for your kind patience and help. As a new user
i am facing some problems and not clear about many options and how to use
them. I was reading several messages of yours from mailing list which are
very close to my problem.
After reading several of them from mailing list i have carefully tuned my
md.mdp file and the energy out put from g_energy is here.

+++++++++++++++++++++++++++++++++++++++++++++++++++

Last energy frame read 1000 time 2000.000

Statistics over 1000001 steps [ 0.0000 thru 2000.0001 ps ], 1 data sets
All averages are exact over 1000001 steps

Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift
-------------------------------------------------------------------------------
Total Energy               -55074.6    348.391    347.979 -0.0293271
-58.6543
+++++++++++++++++++++++++++++++++++++++++++++++++++++++

Energy looks pretty stable compare to the one i have reported in Bugzilla,
in which i always use to get the drift from 200 to 600, and finally it ends
up with positive energy.

Here is the md.mdp file i have used for my current simulation.

++++++++++++++++++++++++++++++++++++++++++++
title           = AB2130
cpp             = /usr/bin/cpp
constraints     = all-bonds
integrator      = md
dt              = 0.002 ; ps !
nsteps          = 1000000 ; total 100.0 ns.
nstxout         = 1000 ; collect data     every 2.0 ps
nstvout         = 1000 ; collect velocity every 2.0 ps
nstfout         = 0
nstlog          = 0
comm_mode       = none
nstenergy       = 1000 ; collect energy   every 2.0 ps
nstlist         = 10
ns_type         = grid
pbc             = xyz
rlist           = 1.0
coulombtype     = cut-off
rcoulomb        = 1.0
rvdw            = 1.0
rvdw_switch     = 0.9
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
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
;Generate velocites is on at 300 K.
gen_vel         = yes
gen_temp        = 283.0
energygrps      = Tmp1 Tmp2
energygrp_excl  = Tmp2 Tmp2 Tmp2 Tmp1
gen_seed        = 181726
freezegrps      = Tmp2
freezedim       = Y Y Y
+++++++++++++++++++++++++++++++++++++++++++++++

I still have small question here, when i try to print the velocities from
trajectory i found that some of the frozen water too get the velocities (i
have complied my gromcas with md.c
Fixed velocity output at first step on nodes>1 with PD and frozen groups).

Here is the example for few frozen water.

++++++++++++++++++++++++++++++++++++++++++++++
   48SOL     OW  149   1.630   1.491   6.061    -0.0001 -0.0000 -0.0000
   48SOL    HW1  150   1.555   1.541   6.027    -0.0001  0.0001 -0.0000
.
.
.
 9503SOL     OW31669   6.075   6.430   0.097    0.0001  0.0000 -0.0000
 9503SOL    HW131670   5.984   6.437   0.126    0.0000  0.0001 -0.0000
 9503SOL    HW231671   6.089   6.508   0.044   -0.0001  0.0001 -0.0000
++++++++++++++++++++++++++++++++++++++++++++++++++

I am not very clear why i am still getting this velocity, and how would
these velocities to frozen atoms effect the simulation?

Can you please give me your suggestions.

Thanks in advance
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
**********************************************
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