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

[Berk Hess]

Hi,

So the system seems to be stable now?

The water molecules might get a very small velocity, because constraints are always applied.
If your starting coordinates do not have full precision (e.g. gro or pdb), a minor correction
and thus velocity will occur at step 0 only. This should not be an issue.

Berk

Date: Sun, 25 Apr 2010 11:59:36 -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, 

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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