[gmx-users] gromacs.org_gmx-users Digest, Vol 187, Issue 49
hind ahmed
aa.hind at hotmail.com
Thu Nov 21 13:22:20 CET 2019
Thanks for your answer
I added -s topol.tpr to the command but I got this warning
WARNING: Oversubscribing the available 40 logical CPU cores with 256 threads.
This will cause considerable performance loss!
Compiled SIMD instructions: AVX_256 (Gromacs could use AVX2_256 on this machine, which is better)
I am running replica exchange simulation for Coarse grained system. is there any special setting to fix this?
thanks
Get Outlook for Android<https://aka.ms/ghei36>
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Today's Topics:
1. replica exchange with GROMACS (hind ahmed)
2. multidir, Segmentation fault (Tamas Hegedus)
3. Re: replica exchange with GROMACS (David de Sancho)
4. Chain length of a polymer (Shan Jayasinghe)
5. Re: Charmm27 and Charmm36 atomtypes assignments for polymer
(Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Wed, 20 Nov 2019 15:19:18 +0000
From: hind ahmed <aa.hind at hotmail.com>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] replica exchange with GROMACS
Message-ID:
<DB8PR10MB3691A1038C2024A385CA3DD9EA4F0 at DB8PR10MB3691.EURPRD10.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="us-ascii"
Hello
Could you please direct me to how can I run job of replica exchange with GROMACS. I used the setting bellow to submit the job on HEC, the job works but with no replex exchange and i got the note below.
#run the md
Mpirun -np 16 mdrun_mpi_d -multidir rep_0 rep_1 rep_2 rep_3 rep_4 rep_5 rep_6 rep_7 rep_8 rep_9 rep_10 rep_11 rep_12 rep_13 rep_14 rep_15 -replex 100
Is there any guide to how i run it right?
NOTE: The number of threads is not equal to the number of (logical) cores
and the -pin option is set to auto: will not pin thread to cores.
This can lead to significant performance degradation.
Consider using -pin on (and -pinoffset in case you run multiple jobs).
Tthanks
------------------------------
Message: 2
Date: Wed, 20 Nov 2019 22:33:05 +0100
From: Tamas Hegedus <tamas at hegelab.org>
To: gmx-users at gromacs.org
Subject: [gmx-users] multidir, Segmentation fault
Message-ID: <dc5676dd-4f6f-7ecd-961d-b4a272df5448 at hegelab.org>
Content-Type: text/plain; charset=utf-8; format=flowed
Hi,
I ran two equilibration simulations to generate two production tpr with
different velocities.
mdrun_mpi runs fine with each tpr (no explosion, the systems are stable).
However, if I set the multidir option, I get segmentation fault.
My system: Debian Buster, GROMACS 2018.6
Thanks for your suggestions,
Tamas
[myhost:39226] Signal: Segmentation fault (11)
[myhost:39226] Signal code: Address not mapped (1)
[myhost:39226] Failing at address: 0x7f94b42e0008
[myhost:39226] [ 0]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x12730)[0x7f94ab991730]
[myhost:39226] [ 1]
/usr/lib/x86_64-linux-gnu/pmix/lib/pmix/mca_gds_ds21.so(+0x2936)[0x7f94a9f72936]
[myhost:39226] [ 2]
/usr/lib/x86_64-linux-gnu/libmca_common_dstore.so.1(pmix_common_dstor_init+0x9d3)[0x7f94a9f62733]
[myhost:39226] [ 3]
/usr/lib/x86_64-linux-gnu/pmix/lib/pmix/mca_gds_ds21.so(+0x25b4)[0x7f94a9f725b4]
[myhost:39226] [ 4]
/usr/lib/x86_64-linux-gnu/libpmix.so.2(pmix_gds_base_select+0x12e)[0x7f94aa0a946e]
[myhost:39226] [ 5]
/usr/lib/x86_64-linux-gnu/libpmix.so.2(pmix_rte_init+0x8cd)[0x7f94aa06188d]
[myhost:39226] [ 6]
/usr/lib/x86_64-linux-gnu/libpmix.so.2(PMIx_Init+0xdc)[0x7f94aa01dd7c]
[myhost:39226] [ 7]
/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext2x.so(ext2x_client_init+0xc4)[0x7f94aa113fe4]
[myhost:39226] [ 8]
/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_pmi.so(+0x2656)[0x7f94aade3656]
[myhost:39226] [ 9]
/usr/lib/x86_64-linux-gnu/libopen-rte.so.40(orte_init+0x29a)[0x7f94aaedc11a]
[myhost:39226] [10]
/usr/lib/x86_64-linux-gnu/libmpi.so.40(ompi_mpi_init+0x252)[0x7f94abbbbe62]
[myhost:39226] [11]
/usr/lib/x86_64-linux-gnu/libmpi.so.40(PMPI_Init_thread+0x55)[0x7f94abbea2d5]
[myhost:39226] [12]
/opt/gromacs-2018.6/bin/mdrun_mpi(+0x41e585)[0x55efb99a9585]
[myhost:39226] [13]
/opt/gromacs-2018.6/bin/mdrun_mpi(+0x3da4d9)[0x55efb99654d9]
[myhost:39226] [14]
/opt/gromacs-2018.6/bin/mdrun_mpi(+0xff6f9)[0x55efb968a6f9]
[myhost:39226] [15]
/opt/gromacs-2018.6/bin/mdrun_mpi(+0xff919)[0x55efb968a919]
[myhost:39226] [16]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xeb)[0x7f94ab7e209b]
[myhost:39226] [17]
/opt/gromacs-2018.6/bin/mdrun_mpi(+0xd4b7a)[0x55efb965fb7a]
[myhost:39226] *** End of error message ***
--
Tamas Hegedus, PhD
Senior Research Fellow
Department of Biophysics and Radiation Biology
Semmelweis University | phone: (36) 1-459 1500/60233
Tuzolto utca 37-47 | mailto:tamas at hegelab.org
Budapest, 1094, Hungary | http://www.hegelab.org
------------------------------
Message: 3
Date: Wed, 20 Nov 2019 23:19:46 +0100
From: David de Sancho <david.desancho at ehu.eus>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] replica exchange with GROMACS
Message-ID:
<CALUsGp2fCOc4E6ehPCvYpX7EFuzrkfiKpYWihg78d7WjJj3QBg at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi
If I may answer your question, you are missing the name of your run input
file, which should be inside each of these directories. So in case you have
the set of tpr files and they are clalled run.tpr in the correct location,
adding -s run.tpr to the command should do the trick. You can find more
instructions here
http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html
All the best,
David
On Wed, 20 Nov 2019 at 16:35, hind ahmed <aa.hind at hotmail.com> wrote:
>
> Hello
> Could you please direct me to how can I run job of replica exchange
> with GROMACS. I used the setting bellow to submit the job on HEC, the job
> works but with no replex exchange and i got the note below.
> #run the md
> Mpirun -np 16 mdrun_mpi_d -multidir rep_0 rep_1 rep_2 rep_3 rep_4
> rep_5 rep_6 rep_7 rep_8 rep_9 rep_10 rep_11 rep_12 rep_13 rep_14
> rep_15 -replex 100
> Is there any guide to how i run it right?
>
> NOTE: The number of threads is not equal to the number of (logical) cores
>
> and the -pin option is set to auto: will not pin thread to cores.
> This can lead to significant performance degradation.
> Consider using -pin on (and -pinoffset in case you run multiple
> jobs).
>
>
> Tthanks
> --
> 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
>
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>
--
David De Sancho <https://sites.google.com/view/daviddesanchoresearch>
Ram?n y Cajal Fellow (UPV/EHU)
Donostia International Physics Center
Manuel Lardizabal Ibilbidea, 4
20018 San Sebastian, Spain
Tel: +34 943018527
------------------------------
Message: 4
Date: Thu, 21 Nov 2019 11:40:09 +1100
From: Shan Jayasinghe <shanjayasinghe2011 at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Chain length of a polymer
Message-ID:
<CAChmq0hc-Wt8KhTzGWsffU5-M6ksowwyicMivGxtnX5Or0LOTQ at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Dear Gromacs Users,
I have a polymer molecule in my MD simulation and I want to calculate how
chain length varies with simulation time. How can I do that with Gromacs
software? Can I use gmx distance? Do I need to create a group with backbone
atoms of the polymer chain in the index file for the calculation?
Appreciate your help.
Thank you.
--
Best Regards
Shan Jayasinghe
------------------------------
Message: 5
Date: Wed, 20 Nov 2019 20:19:16 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments
for polymer
Message-ID: <7db2548d-f487-a34b-f27f-0f876aa202ca at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 11/19/19 9:54 PM, Mijiddorj B wrote:
> Dear Gmx users,
>
> Currently, I am trying to assign the atomtypes in charmm27 for the
> polyethyleneimine polymer. It includes several different groups of atoms. I
> included following illustration and asignment:
> ##############################################
> H CH2
> | /
> NH2--CH2--CH2--N--CH2--CH2--N--CH2 ...
>
> ##############################################
> I assigned and the charmm27 atomtypes as following and compared charmm36
> atomtypes generated by CgenFF.
> Atom Charmm27 Charmm36
> N (NH2) ---> NH2 | NG321
> N (NH1) ---> NH1 | NG311
> C (CH2) ---> CT2 | CG321
> H (HC2) ---> HA | HGA2
> N ? | NG301
>
> If you have any experience, please check my assignments the charmm27 atom
> types and advice me the atomtype of the last Nitrogen, which were assigned
> as NG301 with CgenFF.
Why are you replacing the CGenFF atom types? The replacements you are
making completely change the LJ terms and therefore render the dihedral
parameters invalid. There is no need to make these changes, just use the
CGenFF atom types in your simulation (all of which is contained in the
CHARMM36 port, which you should use rather than the outdated CHARMM27
force field files).
-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
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
------------------------------
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