[gmx-users] Re: Salt-bridge segmentation fault

Justin Lemkul jalemkul at vt.edu
Thu Feb 7 13:01:01 CET 2013

On 2/7/13 6:42 AM, Kavyashree M wrote:
> Dear users,
> After simulation dimers appear separated, I was
> able to do saltbridge calculation on this. This will
> be different than doing it on a dimer which are together.
> Am I correct?

Most Gromacs tools handle PBC well for simple metrics like measurements.  I 
would suspect that the seg fault comes from a mismatch in the .tpr and .xtc 
contents.  g_saltbr is a rather stupid tool that tries to guess salt bridges 
based on anything that's charged, which includes ions and other groups that 
don't necessarily participate in such interactions (see the discussion on this 
same topic in recent days).  Perhaps if g_saltbr is identifying elements that it 
wants to examine from the .tpr file but can't find them in the trajectory, you 
get a seg fault.  This shouldn't happen, but you can also use tpbconv to produce 
a subset .tpr file with just the protein for the purposes of analysis.


> On Thu, Feb 7, 2013 at 3:39 PM, Kavyashree M <hmkvsri at gmail.com> wrote:
>> Dear users,
>> While calculating salt bridges using g_saltbr I got
>> segmentation fault when I used trajectory with only
>> the protein. But when I used the trajectory with
>> water It worked. But the problem was that the
>> monomers were far apart in the trajectory with water
>> and not with the only-protein trajectory.
>> Kindly help!
>> Thank you
>> Kavya


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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