----- Original Message -----
From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Saturday, June 19, 2010 2:48 am
Subject: Re: [AMBER] problem with the energetics of the system
To: amber.ambermd.org
> Homa,
>
> > I heat the system step by step from 0 to 308 K
> > for about 20 ps, after minimizition.
>
> Stepwise warming is good. How about NVT vs. NPT?
> If you send your mdin files, we can check more
> in detail. 20ps seems a little short for a big
> system. Did you graph e.g. density and rms?
do you mean mdin files is this (the below lines)?
&cntrl
imin = 0, irest = 1, iwrap=1 ,ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
tempi = 308.0, temp0 = 308.0,
ntt = 1, gamma_ln = 0,
nstlim = 100000, dt = 0.002,
ntpr = 100, ntwx = 500, ntwr = 1000
> > the below message came after 48 ns.
> > also my system is a dimer protein with one ligand.
>
> I assume that's 48 ps?
this message came after 48 ns. my jobs was a series of 200ps so after 240 run this message came.So the run 240 is stoped. and I also check the mdcrd from run 239 by VMD, I saw a long bond in one residue, which it didnt occure in run 238.
What should I do for fixing the problem of defected bond?
I should also said that I add iwrap=1 for getting 239.rst, and by adding this I saw that the xyz of the protein changes.
> In such cases the ligand parameterization is the main suspect,
> but my impression is that usually it happens sooner if this is
> the case. Another possibility that occurs to me is that you might
> be restarting with the wrong restrt file or mdin.
I also run a simulation of the same system with 2 ligand (this was with one ligand), and it finished succesfully, so I think it not because of the parametrization of ligand.
> > vlimit exceeded for step 0; vmax = 388.4665
> > vlimit exceeded for step 1; vmax = 399.4700
> > vlimit exceeded for step 2; vmax = 387.9217
> > vlimit exceeded for step 3; vmax = 352.8459
> > vlimit exceeded for step 4; vmax = 32817.3873
> > Coordinate resetting (SHAKE) cannot be accomplished,
> > deviation is too large
> > NITER, NIT, LL, I and J are : 0 3 302 606 607
> > Note: This is usually a symptom of some deeper
> > problem with the energetics of the system.
>
> I think atoms 606, 607 are the problem here. One thing you could try
> is to save every step to mdcrd and watch what happens in a dynamics
> viewer like VMD.
>
> Bill
>
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Received on Fri Jun 18 2010 - 23:30:03 PDT
