Are you able to determine which atom actually had the velocity limit
issue? I'm assuming it was the magnesium, but maybe that isn't true.
Also, I assume from what you've written that this is in water with
counterions and your protein. Did you try just the ATP + Mg in a vacuum
first? It might be helpful to start there, and then move to just the ATP +
Mg in a small box of water, and then finally integrate the whole system.
One other note, as was brought up by Brian, is there a particular reason
that you are choosing NVE ensemble rather than NTP?
~Aron
On Tue, Dec 13, 2011 at 10:41 AM, Xiaozhou Li <xli12.qub.ac.uk> wrote:
> Hi Brian,
>
> Many thanks for your reply. I'll following the point you've raised to make
> a discussion below.
>
> 1) Well, exactly. Magnesium parameters varies a lot depending on the
> system we considering. I've looked up some literatures to see whether
> similar system existed as it wasn't a brand-new coordinating environment.
> Several groups of data were obtained but none of them was suitable for my
> system. Anyway this review-and-try work is still on processing.
>
> 2) For a macromolecule system, 5000 steps of minimization is relatively a
> common one. Actually I've tried 1000 steps of minimization but still failed.
>
> 3) Enzymes usually works on a proper temperature (for example, body
> temperature), and that is why I should make the heating step-- make the
> simulation more reliable. There's no velocity data obtained from
> minimization step. Other trials with tempi=10, =20, =30 were conducted
> and... all failed with the same problem (vlimit exceeded). Plus, the
> reference temperature could not be ignored as another trial mentioned at
> the last of my first post, everything went fine when utilizing the same
> simulation conditions in MD step.
>
> Starting with a desired temperature for a large system doesn't work and
> the reason is just what you said.
>
> Thanks in advance,
> Xiaozhou
> ________________________________________
> From: Brian Radak [radak004.umn.edu]
> Sent: 13 December 2011 15:04
> To: AMBER Mailing List
> Subject: Re: [AMBER] vlimit exceeded issue
>
> A few things that may hopefully address your problems:
>
> 1.) Magnesium parameters are generally considered to be highly application
> dependent. I don't think anyone in the AMBER community has advocated a
> single "best" set yet. You probably want to carefully search the
> literature and run some basic tests before settling on a model. It
> probably won't be one that is released with AMBER (i.e. is already in a
> parm or frcmod file).
>
> 2.) In my opinion, and others here might agree, 5000 steps of minimization
> is rather extraneous and probably more likely to cause new problems than
> resolve old ones. 1000 TOTAL is probably a more useful value.
>
> 3.) I'm not sure what you were meaning to do with your heating. As is, you
> are specifying 0 initial temperature (tempi) so that all velocities are
> zero (probably not good). The reference temperature (temp0) will probably
> be ignored since you specified NVE dynamics (ntt=1), but I don't know for
> sure.
>
> There are many many heating procedures that you could use, but I don't know
> enough to recommend you a specific. For small molecules I've had
> reasonable success with just starting at the desired temperature, but I
> think that may fail for larger systems, especially if the initial
> coordinates are from a low temperature crystal structure.
>
> Regards,
> Brian
>
> On Tue, Dec 13, 2011 at 9:23 AM, Xiaozhou Li <xli12.qub.ac.uk> wrote:
>
> > Dear AMBER users,
> >
> > I'm now working on a MD simulation to an enzyme which has peculiar
> > ligands. Followed the official tutorial which dealing with non-standard
> > residue (link: http://ambermd.org/tutorials/advanced/tutorial1_adv/) I
> > created a new residue "ATP" which contains an ATP as well as a magnesium
> > ion (nominated as "MG" and it does not exist in the library).
> >
> > The template of the new residue was first generated by Gaussian 09 (by
> > single point charge calculation), then use "antechamber" in AMBER to
> shift
> > it into ".mol2" format, which contains atom charges and connection
> > information, etc. A ".frcmod" file was created simultaneously, said that
> > the MASS and NONBON parameters of MG should be revised. MASS was pretty
> > easy to obtain, NONBON was directly use those original information in
> AMBER
> > lib.
> >
> > In "tleap", the residue I manually created was imported directly by the
> > command "loadmol2". The final model for simulation was then successfully
> > generated. The minimization step was OK, using 5000 step of SD method as
> > well as 5000 step of CONJ method without restriction to the protein.
> Issue
> > occurred when it came to the starting point of heating step:
> >
> > (the last lines in the output file)
> > vlimit exceeded for step 3; vmax = 21.5763
> > vlimit exceeded for step 4; vmax = 115.6802
> > vlimit exceeded for step 5; vmax = 221.8382
> > vlimit exceeded for step 6; vmax = 74.7778
> > vlimit exceeded for step 7; vmax = 42.8791
> >
> > Here are the ".frcmod" file and my MD input condition:
> >
> >
> >
> > (.frcmod file)
> >
> > ------------------------------------------------
> > remark goes here
> > MASS
> > MG 24.305
> >
> > BOND
> >
> > ANGLE
> >
> > DIHE
> >
> > IMPROPER
> > c3-ca-na-cc 1.1 180.0 2.0 Using default
> > value
> > h5-na-cc-nd 1.1 180.0 2.0 Using default
> > value
> > ca-ca-ca-nd 1.1 180.0 2.0 Using default
> > value
> > ca-nb-ca-nh 1.1 180.0 2.0 Using default
> > value
> > ca-hn-nh-hn 1.1 180.0 2.0 Using default
> > value
> > h5-nb-ca-nb 1.1 180.0 2.0 Using default
> > value
> > ca-na-ca-nb 1.1 180.0 2.0 Using default
> > value
> >
> > NONBON
> > MG 0.7926 0.8947 ATTN, need revision
> > ------------------------------------------------
> > (MD input file)
> > ------------------------------------------------
> > Heating
> > &cntrl
> > imin=0,irest=0,ntx=1,ntb=1,
> > cut=10.0,ntr=1,restraint_wt=0.5,restraintmask=':1-395',
> > ntc=2,ntf=2,
> > tempi=0.0,temp0=300.0,
> > ntt=1,nstlim=50000,dt=0.001,ntpr=100,ntwx=100,ntwr=200
> >
> > I'm pretty appreciated if anyone could help me to get through that issue.
> >
> > P.S. In my previous work, I utilized the normal template which exist in
> > the AMBER lib (name: MG2) for the magnesium ion. The template of ATP did
> > not contain the magnesium ion. The ".frcmod" file corresponding to ATP
> was
> > just as the one I provided above, but without information on MG.
> Everything
> > went fine from minimization to heating, equilibration and MD simulation
> > with NPT ensemble. Hopefully what I mention here make sense.
> >
> > Many thanks,
> > Xiaozhou
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
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Received on Tue Dec 13 2011 - 08:00:05 PST
