[gmx-users] What might be the best way of analysis of this kind of salt bridges with Gromacs?

Justin Lemkul jalemkul at vt.edu
Mon Apr 29 14:26:01 CEST 2019

On 4/24/19 6:57 AM, Anna VERDINO wrote:
> Dear Gromacs users,
> I have a dimeric protein and I am interested in analysing the salt bridges
> between chain A and B.
> When I do this command:
> *gmx saltbr [-f [<.xtc/.trr/...>]] [-s [<.tpr>]]*
> after a while it is killed.
> I just tryed to do this command using only a frame of trajectory:
> *gmx saltbr [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-b <time>] [-e <time>] *
> but it is killed again.
> This is error output:
> *Reading file topol.tpr, VERSION 2018.2 (single precision)**
> /var/spool/slurmd/job1310742/**slurm_script: line 18: 22509 Killed
>                   gmx saltbr -f trj.xtc -s topol.tpr -b 0 -e 20000*
> * slurmstepd: error: Detected 1 oom-kill event(s) in step 1310742.batch
> cgroup. Some of your processes may have been killed by the cgroup
> out-of-memory handler.*
> I understand that the problem is the memory requirement. However, I don't
> want to calculate ALL the salt bridges present in the protein, but only
> those involved in interchain interactions. What might be the best way of
> analysis of this kind of salt bridges with Gromacs? It seems to me that
> with gmx saltbr I cannot specify a subgroup of residues by using -n.
> Can anyone help me?

gmx saltbr requires a huge amount of memory as it considers any pair of 
charges (including mobile ions!) as being capable of participating in a 
salt bridge. The more judicious approach is to specifically study 
interatomic distances of interest, identified by prior knowledge of the 
structure and what you observe while watching the trajectory.



Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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