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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>
> 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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> --
> 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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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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