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
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
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jalem...@vt.edu | (540) 231-3129
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