[gmx-users] Re: gmx-users Digest, Vol 48, Issue 82

Bonner, Carl E. cebonner at nsu.edu
Thu Apr 24 15:39:15 CEST 2008 

A
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Date: Thu, 24 Apr 2008 08:22:48 
To:<gmx-users at gromacs.org>
Subject: gmx-users Digest, Vol 48, Issue 82


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 Today's Topics:
 
    1. AFMM parameter refinement (Abu Naser)
    2. Re: position restraints (chandrabhan seniya)
 
 
 ----------------------------------------------------------------------
 
 Message: 1
 Date: Thu, 24 Apr 2008 12:15:36 +0000
 From: Abu Naser <likhonnaser at hotmail.com>
 Subject: [gmx-users] AFMM parameter refinement
 To: <gmx-users at gromacs.org>
 Message-ID: <BAY134-W280AD67632750D9153BEE2A3E20 at phx.gbl>
 Content-Type: text/plain; charset="iso-8859-1"
 
 
 Hi All,
 
 Has any body tried doing parameter refinement using Vaiana's python code
called afmm.py?
 
 A.C. Vaiana, Z. Cournia, I.B. Costescu and J.C. Smith, "AFMM: A molecular
mechanics force field vibrational parametrization program'", Computer Physics
Communications, 167 (2005), pp.34-42.
 
 I have done a test run  using propene setup that came along with the code
and came across a problem. It gives me the same minimum and current sigma
value in every steps as:
 Minimum sigma: 5782.258565, current sigma: 5782.258565
 
 Dose anybody know what might be the problem?
 
 With regards,
 
 Abu
 
 
 
 
 
 
 
 _________________________________________________________________
 Be a superhero and win! Play the Iron Man Mashup Game
 http://www.ironmanmashup.co.uk <http://www.ironmanmashup.co.uk> 
 
 ------------------------------
 
 Message: 2
 Date: Thu, 24 Apr 2008 17:52:09 +0530
 From: "chandrabhan seniya" <chandrabhanseniya at gmail.com>
 Subject: Re: [gmx-users] position restraints
 To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
 Message-ID:
         <bfe51e7a0804240522i6d7bfab6mabd798045b8c2ba1 at mail.gmail.com>
 Content-Type: text/plain; charset="utf-8"
 
 what is yr real prob tell me?
 
 
 On Thu, Apr 24, 2008 at 5:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
 
 > Quoting chandrabhan seniya <chandrabhanseniya at gmail.com>:
 >
 > > no prob you wait for some time it will write topology file and the
 > proceed
 > > further..
 >
 > I think that a lipid molecule trying to tear itself apart at step 0 would
 > fall
 > under the category of a "problem," and it will not disappear on it's own
 > if we
 > conveniently ignore it...
 >
 > >
 > > On Thu, Apr 24, 2008 at 5:04 PM, <gadies at fh.huji.ac.il> wrote:
 > >
 > > > Hi,
 > > >
 > > > The full mdrun output when the simulation blows up is:
 > > >
 > > > Step 0, time 0 (ps)  LINCS WARNING
 > > > relative constraint deviation after LINCS:
 > > > max inf (between atoms 6 and 7) rms inf
 > > > bonds that rotated more than 30 degrees:
 > > >         .
 > > >         .
 > > >         .
 > > > Warning: 1-4 interaction between 1 and 6 at distance
 > > > 324490777485109120.000 which is larger than the 1-4 table size 1.000
 > nm
 > > > These are ignored for the rest of the simulation
 > > > This usually means your system is exploding,
 > > > if not, you should increase table-extension in your mdp file
 > > >
 > > > Thanks Gadi
 > > >
 > > > Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
 > > >
 > > >
 > > > > Did your minimization converge to a nice, negative potential energy?
 > > > >  Also, what
 > > > > is the full mdrun output when the simulation blows up?  You've
 >  quoted
 > > > > the last
 > > > > bit, but it would be more informative to see the whole output, or at
 > > > > least a
 > > > > description of it (i.e., LINCS warnings).
 > > > >
 > > > > -Justin
 > > > >
 > > > > Quoting gadies at fh.huji.ac.il:
 > > > >
 > > > >
 > > > > > Hi,
 > > > > >
 > > > > > I tried using no temperature coupling and no constraints, that did
 > not
 > > > > > help.
 > > > > > If I run the simulation without the position restraints it works
 > OK.
 > > > > > Could there by something wrong with the posre file (I'll attach it
 > at
 > > > > > the end of the email).
 > > > > > I want one of the atoms in the lipid to stay in one place and the
 > rest
 > > > > > to wiggle around it. Is there any other way to do that which is
 > not
 > > > > > position restraints.
 > > > > >
 > > > > > Thanks Gadi
 > > > > >
 > > > > >
 > > > > > [ position_restraints ]
 > > > > > ; atom  type      fx      fy      fz
 > > > > >      1     1  0  0  0
 > > > > >      2     1  0  0  0
 > > > > >      3     1  0  0  0
 > > > > >      4     1  0  0  0
 > > > > >      5     1  0  0  0
 > > > > >      6     1  0  0  0
 > > > > >      7     1  0  0  0
 > > > > >      8     1  1000.0  1000.0  1000.0
 > > > > >      9     1  0  0  0
 > > > > >     10     1  0  0  0
 > > > > >     11     1  0  0  0
 > > > > >     12     1  0  0  0
 > > > > >     13     1  0  0  0
 > > > > >     14     1  0  0  0
 > > > > >     15     1  0  0  0
 > > > > >     16     1  0  0  0
 > > > > >     17     1  0  0  0
 > > > > >     18     1  0  0  0
 > > > > >     19     1  0  0  0
 > > > > >     20     1  0  0  0
 > > > > >     21     1  0  0  0
 > > > > >     22     1  0  0  0
 > > > > >     23     1  0  0  0
 > > > > >     24     1  0  0  0
 > > > > >     25     1  0  0  0
 > > > > >     26     1  0  0  0
 > > > > >     27     1  0  0  0
 > > > > >     28     1  0  0  0
 > > > > >     29     1  0  0  0
 > > > > >     30     1  0  0  0
 > > > > >     31     1  0  0  0
 > > > > >     32     1  0  0  0
 > > > > >     33     1  0  0  0
 > > > > >     34     1  0  0  0
 > > > > >     35     1  0  0  0
 > > > > >     36     1  0  0  0
 > > > > >     37     1  0  0  0
 > > > > >     38     1  0  0  0
 > > > > >     39     1  0  0  0
 > > > > >     40     1  0  0  0
 > > > > >     41     1  0  0  0
 > > > > >     42     1  0  0  0
 > > > > >     43     1  0  0  0
 > > > > >     44     1  0  0  0
 > > > > >     45     1  0  0  0
 > > > > >     46     1  0  0  0
 > > > > >     47     1  0  0  0
 > > > > >     48     1  0  0  0
 > > > > >     49     1  0  0  0
 > > > > >     50     1  0  0  0
 > > > > >
 > > > > > Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:
 > > > > >
 > > > > > > gadies at fh.huji.ac.il wrote:
 > > > > > >
 > > > > > > Please generate replies to the mailing list sensibly. It's very
 > hard
 > > > > > to
 > > > > > > work out who you are quoting where in this email. It'd be easy
 > just
 > > > > > to
 > > > > > > ignore it, and that's the last thing you should want.
 > > > > > >
 > > > > > >> Hello,
 > > > > > >>
 > > > > > >> I'm trying to run a simulation with one lipid molecule in a
 > fixed
 > > > > > >> simulation box without pbc.
 > > > > > >> I set position restraints on one of the atoms and I seem to
 > keep on
 > > > > > >> getting the following error:
 > > > > > >
 > > > > > > Why do you want MD of a single lipid and a position restraint on
 > one
 > > > > > > atom? If you just want to see a lipid wiggle around, then don't
 > > > > > create
 > > > > > > more numerical complexity.
 > > > > > >
 > > > > > >> The lipid is DPPC.The .itp file I got from a coworker that used
 > it
 > > > > > >> before for membrane MD simulations.
 > > > > > >> To minimize the system I used steepest descent with the
 > following
 > > > > > >> parameters:
 > > > > > >
 > > > > > > Well if your grompp and mdrun completed successfully and without
 > > > > > > warnings then you've probably got an OK topology and structure.
 > > > > > >
 > > > > > > The combination of all bond constraints, a single lipid in
 > vacuo,
 > > > > > > temperature coupling and a single position restraint sounds like
 > a
 > > > > > > recipe for a numerical disaster, i.e. blowing up. Try with fewer
 > of
 > > > > > > those things applied, or get a more physically-reasonable
 > system,
 > > > > > like
 > > > > > > a whole membrane.
 > > > > > >
 > > > > > > Mark
 > > > > > > _______________________________________________
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 > > > > >
 > > > > >
 > > > > >
 > > > > > ----------------------------------------------------------------
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 > > > > >
 > > > > > _______________________________________________
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 > > > > >
 > > > > >
 > > > >
 > > > >
 > > > > ========================================
 > > > >
 > > > > Justin A. Lemkul
 > > > > Graduate Research Assistant
 > > > > Department of Biochemistry
 > > > > Virginia Tech
 > > > > Blacksburg, VA
 > > > > jalemkul at vt.edu | (540) 231-9080
 > > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> 
 > > > >
 > > > > ========================================
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 > > > >
 > > >
 > > >
 > > > ----------------------------------------------------------------
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 > > >_______________________________________________
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 > > >
 > >
 >
 >
 >
 > ========================================
 >
 > Justin A. Lemkul
 > Graduate Research Assistant
 > Department of Biochemistry
 > Virginia Tech
 > Blacksburg, VA
 > jalemkul at vt.edu | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> 
 >
 > ========================================
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