From owner-chemistry@ccl.net Thu Sep 30 08:45:00 2021 From: "Shivangi Gupta shivigupta216[]gmail.com" To: CCL Subject: CCL: About MD simulation using GROMACS software Message-Id: <-54465-210930032654-29841-NeQ4CVwPFvtWq3VvBfms9w\a/server.ccl.net> X-Original-From: Shivangi Gupta Content-Type: multipart/alternative; boundary="000000000000958ee705cd315e4e" Date: Thu, 30 Sep 2021 12:56:37 +0530 MIME-Version: 1.0 Sent to CCL by: Shivangi Gupta [shivigupta216^_^gmail.com] --000000000000958ee705cd315e4e Content-Type: text/plain; charset="UTF-8" Respected Sir / Ma'am, I am a new person in the field of MD simulation. I want to learn how to do the MD simulation using GROMACS software. please provide me some suggestion in this regard. --000000000000958ee705cd315e4e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Respected Sir / Ma'am,=C2=A0
I am a new person in = the field of MD simulation. I want to learn how to do the MD simulation usi= ng GROMACS software. please provide me some suggestion in this=C2=A0regard.=
--000000000000958ee705cd315e4e-- From owner-chemistry@ccl.net Thu Sep 30 10:51:00 2021 From: "Kshatresh Dutta Dubey kshatresh%%gmail.com" To: CCL Subject: CCL: About MD simulation using GROMACS software Message-Id: <-54466-210930104926-23661-HfSqtxU3xdhg4tleymIQ4A * server.ccl.net> X-Original-From: Kshatresh Dutta Dubey Content-Type: multipart/alternative; boundary="00000000000040670205cd378d28" Date: Thu, 30 Sep 2021 20:19:09 +0530 MIME-Version: 1.0 Sent to CCL by: Kshatresh Dutta Dubey [kshatresh===gmail.com] --00000000000040670205cd378d28 Content-Type: text/plain; charset="UTF-8" There is a very good tutorial by Justin Lemkul. http://www.mdtutorials.com/gmx/ Please go through it. On Thu, 30 Sep 2021 at 7:58 PM, Shivangi Gupta shivigupta216[]gmail.com < owner-chemistry ~~ ccl.net> wrote: > Respected Sir / Ma'am, > I am a new person in the field of MD simulation. I want to learn how to do > the MD simulation using GROMACS software. please provide me some suggestion > in this regard. > -- With best regards ************************************************************************************************ Dr. Kshatresh Dutta Dubey Department of Chemistry School of Natural Sciences Shiv Nadar University Gautam Budhha Nagar Uttar Pradesh-201314 India --00000000000040670205cd378d28 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
There is a very good tutorial by Justin Lemkul.=C2=A0
Please go th= rough it.=C2=A0

On Thu, 30 Sep 2021 at 7:58 PM, Shivangi Gupta shivigup= ta216[]gmail.com <owner-chemistry ~~ ccl.net> wrote:
Respected Sir / Ma'am,=C2=A0
I am a ne= w person in the field of MD simulation. I want to learn how to do the MD si= mulation using GROMACS software. please provide me some suggestion in this= =C2=A0regard.
--
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With best regards
*********************************= ***************************************************************
Dr. Kshatresh D= utta Dubey
Department of Chemistry=
School of Natural Sciences=
Shiv Nadar University
<= font color=3D"#0000ff">Gautam Budhha Nagar
Uttar Pradesh-201314
Indi= a


=
--00000000000040670205cd378d28-- From owner-chemistry@ccl.net Thu Sep 30 22:58:00 2021 From: "Anson Thomas a_thomas_._cy.iitr.ac.in" To: CCL Subject: CCL: Command to run QE-GPU Message-Id: <-54467-210930220817-12244-uFr9CYZH50mgZFKcIqgvlg[A]server.ccl.net> X-Original-From: "Anson Thomas" Date: Thu, 30 Sep 2021 22:08:14 -0400 Sent to CCL by: "Anson Thomas" [a_thomas**cy.iitr.ac.in] Hello. I have installed quantum espresso with GPU support on a system. Ubuntu 18.04.5 LTS (GNU/Linux 4.15.0-135-generic x86_64) System Configuration: Processor: Intel Xeon Gold 5120 CPU 2.20 GHz (2 Processor) RAM: 96 GB HDD: 6 TB Graphics Card: NVIDIA Quadro P5000 (16 GB) Usually, without GPU support, I submit jobs simply using: mpirun pw.x -inp input.in > output.out. The output file in such cases includes these lines: Parallel version (MPI), running on 28 processors MPI processes distributed on 1 nodes K-points division: npool = 2 R & G space division: proc/nbgrp/npool/nimage = 14 wavefunctions fft division: Y-proc x Z-proc = 2 7 wavefunctions fft division: task group distribution #TG x Z-proc = 2 7 However, I do not understand what additional parameters are to be included while running with GPU support to use it. I read about -ndiag, ntg, npool and other options on the internet but could not understand how to use them for my configuration. I would be really grateful if someone could give more insight into using these options to use GPU in my calculations fully. Thanks in advance.