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

Thu Mar 15 14:30:18 CET 2007

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

  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
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