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

[sangeeta kundu]

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 <tsjerkw at gmail.com> 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 <erikm at xray.bmc.uu.se>
> 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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