[gmx-users] Check for bad contacts and/or reduce the timestep

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Wed Dec 16 19:51:11 CET 2009

Hi Justin,

   I am trying to plot rdf of one methane molecule in water (spc  
water, 1095(water molecule in my file). I did create the file using  
genbox (31.010 31.010 31.010). This is the energy minimization file I  
am using:

title		= Methane in water

cpp		= /lib/cpp
include		= -I../top

integrator	= steep
emtol		= 1.0
nsteps		= 100
nstenergy	= 10
nstxtcout	= 10
xtc_grps	= CH4 SOL
energygrps	= CH4 SOL
nstlist		= 5
ns_type		= simple
rlist		= 1.0
coulombtype	= cut-off
rcoulomb	= 1.0
rvdw		= 1.0
constraints	= none
pbc		= no

I tried reducing the steps (to 9 instead of 100) and it works but it  
doesn't make sense. I am going to try to build the system again.

Thanks alot of for help.


Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

> nishap.patel at utoronto.ca wrote:
>> Hi, I tried energy minimization and I am getting the error while I   
>> am running the minimization step. But then I still tried to carry   
>> on with normal md-simulation, and it was fine, but I am sure it   
>> won't give me the result that it should. Is there a reason for   
>> that? I have tried very low energy steps as well, but I am still   
>> getting the error.
> If minimization still reports the same problems, then what I said
> before is still true - you have bad contacts somewhere.  Have you
> looked at the trajectory to see where these problematic atoms are and
> what might be causing the clashes?
> Sometimes running sufficiently gentle equilibration can relax away some
> of these bad contacts, but that is rarely the case and often problems
> will manifest later on in the course of MD.  I would seriously consider
> re-evaluating however you built your system (which you haven't told us)
> and try to get the energy minimization to actually work before just
> plowing ahead with fingers crossed.
> -Justin
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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