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

[Anna VERDINO]

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?

Many thanks in advance for your kind answer

Anna