[gmx-users] problem regarding "mdrun" and "g_hbond"

[Erik Marklund]

15 mar 2007 kl. 14.30 skrev sangeeta kundu:

> Dear Tsjerk,
>     My protein had -5.99 charge , so I added 6 NA+ atoms, not a  
> single one.
>

Nevertheless, 6 atoms is a very small tc-group. Large fluctuations in  
kinetic energy is expected for such a small collection of atoms,  
making the temperature coupling behave kind of wildly.

/Erik

> regards
> Sangeeta
>
>
> Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Sangeeta,
>
> I think the problem is a lone sodium ion which is shaken vigorously
> round by its private heat bath, at some point getting too intimate
> with one of the water molecules around.
>
> Never, never, NEVER give a handful of atoms, or a single atom, it's
> own heat bath! Put the sodium in with the solvent. Search the archives
> for tc-grps, temperature coupling, and such (and possibly my name), to
> get a fuller account. Besides that, you may be better off adding some
> additional sodium chloride... One sodium may balance the net charge,
> but it will not balance a charged protein.
>
> Cheers,
>
> Tsjerk
>
>
> On 3/15/07, sangeeta kundu wrote:
> > Dear All,
> >
> > Thanks a lot to Mark,Tsjerk and Erik your promt reply.
> > It is a globular protein containing approximately 70
> > residues having crysal structure, without any
> > ligand,the simulation continued for 1.5 ns, & then
> > gave the segmentation fault, My .mdp file is given
> > below, I used SPC216 water and steepest descent for
> > minimisation, the emtol was 1000,it converged to that
> > within 800 steps.I used position restrained dynamics
> > for 50ps.The protein had -ve charge, so I added NA+
> > as counter ion.I used the same parameter
> > for carrying out the simualtion of the same protein at
> > 3/4 other tempeartures,the runs were completed without
> > giving any error.Waiting for your promt help.
> >
> > title = Yo
> > cpp = /usr/bin/cpp
> > constraints = all-bonds
> > integrator = md
> > dt = 0.002 ; ps !
> > nsteps = 5000000 ; total 10 ns
> > nstcomm = 1
> > nstxout = 250
> > nstvout = 1000
> > nstfout = 0
> > nstlog = 100
> > nstenergy = 100
> > nstlist = 10
> > ns_type = grid
> > rlist = 1.0
> > rcoulomb = 1.0
> > rvdw = 1.0
> > ; Berendsen temperature coupling is on in two groups
> > Tcoupl = berendsen
> > tc-grps = Protein SOL NA+
> > tau_t = 0.1 0.1 0.1
> > ref_t = 523 523 523
> > ; Energy monitoring
> > energygrps = Protein SOL
> > ; Isotropic pressure coupling is now on
> > Pcoupl = berendsen
> > Pcoupltype = isotropic
> > tau_p = 0.5
> > compressibility = 4.5e-5
> > ref_p = 1.0
> > ; Generate velocites is off at 300 K.
> > gen_vel = no
> > gen_temp = 523.0
> > gen_seed = 173529
> >
> >
> >
> > regards
> > Sangeeta
> > --- Tsjerk Wassenaar wrote:
> >
> > > Hi Sangeeta,
> > >
> > > It would be helpful to us if you gave more
> > > information than "I tried
> > > to run a simulation and it crashed". What kind of
> > > protein, any
> > > ligands/non-standard groups. Did you perform energy
> > > minimization, etc,
> > > etc, etc... What's in the .mdp file?
> > >
> > > Tsjerk
> > >
> > > On 3/15/07, Erik Marklund
> > > wrote:
> > > >
> > > >
> > > > 15 mar 2007 kl. 08.29 skrev sangeeta kundu:
> > > >
> > > > Dear all,
> > > > I gave a simulation run of a protein using
> > > G43a1force field at 523K
> > > > using Berendson's Temperature coupling for 10
> > > ns, But three times it
> > > > failed with the messege "segmentation fault" ,
> > > without giving any other
> > > > error messege. Previously I ran the simualtion of
> > > the same protein at lower
> > > > temperature, (upto 473K) , and in all cases it ran
> > > successfully, but when I
> > > > used the temperature of 523 K it failed, I can not
> > > debug, please help.
> > > >
> > > >
> > > > I'm no expert, but I think a shorter timestep
> > > could be required for the
> > > > integrator to be stable when using such high
> > > temperatures, since the atoms
> > > > will move around quite fast.
> > > >
> > > >
> > > >
> > > > I have another question, Is there any way of
> > > analysing hydrogen bonds
> > > > on a residue basis? I mean to say how can I get
> > > the distribution of HBond
> > > > over residue number, I looked at g_hbond , but I
> > > could not get it.
> > > >
> > > >
> > > > It requires some postprocessing of the data, but
> > > the hbn- and hbm-output of
> > > > g_hbond together contains what you need to know
> > > about the hydrogen bonds on
> > > > an atom index basis. Now, you can easily go from
> > > the level of atoms to the
> > > > level of residues.
> > > >
> > > >
> > > >
> > > > regards
> > > > Sangeeta
> > > >
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> > > > _______________________________________________
> > > > Erik Marklund, PhD student
> > > > Laboratory of Molecular Biophysics,
> > > > Dept. of Cell and Molecular Biology, Uppsala
> > > University.
> > > > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > > > phone: +46 18 471 4537 fax: +46 18 511 755
> > > > erikm at xray.bmc.uu.se
> > > http://xray.bmc.uu.se/molbiophys
> > > >
> > > >
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> > >
> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> > > Junior UD (post-doc)
> > > Biomolecular NMR, Bijvoet Center
> > > Utrecht University
> > > Padualaan 8
> > > 3584 CH Utrecht
> > > The Netherlands
> > > P: +31-30-2539931
> > > F: +31-30-2537623
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>
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys


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