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

[Justin Lemkul]

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

-- 
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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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