Are you using sander or pmemd? pmemd tends to wrap much better than sander,
if this turns out to be an imaging problem. (it's also uber fast compared to
sander for the subset of capabilities it has)
Good luck!
Jason
On Sat, Jun 19, 2010 at 2:04 AM, Homa Azizian <homa.azizian.anu.edu.au>wrote:
>
>
> ----- 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Jun 19 2010 - 09:00:04 PDT
