Re: [gmx-users] What might be the best way of analysis of this kind of salt bridges with Gromacs?
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 ] [-e ] * 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 2* * 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 -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] What might be the best way of analysis of this kind of salt bridges with Gromacs?
Il Mer 24 Apr 2019, 12:57 Anna VERDINO ha scritto: > 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 ] [-e ] * > 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 2* > * 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 > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] What might be the best way of analysis of this kind of salt bridges with Gromacs?
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 ] [-e ] * 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 2* * 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
