Re: [gmx-users] Free-energy on GMX-2019.1 ( lower performance on GPU) (Mark Abraham)

onded gpu to your mdrun invocation, by moving such work off the CPU. BTW lincs-order=12 is uselessly large, but is not the problem here. Mark On Fri, 15 Mar 2019 at 06:16 praveen kumar wrote: > Dear All > > I am trying to run the free-energy simulation using TI method in gromacs >

[gmx-users] Free-energy on GMX-2019.1 ( lower performance on GPU)

Dear All I am trying to run the free-energy simulation using TI method in gromacs 2019.1 in a GPU machine (containing two Nvidia Geforce 1080 TI cards ). But unfortunately, am unable to run the free-energy simulation run on GPU. The normal MD simulation (without free-energy )is able to run perfe

Re: [gmx-users] multiple GPU usage for simulation

list.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > T

[gmx-users] multiple GPU usage for simulation

would be really thankful to if anyone can help me in this regard. Thanks Praveen -- Thanks & Regards Dr. Praveen Kumar Sappidi, National Post Doctoral Fellow. Computational Nanoscience Laboratory, Chemical Engineering Department, IIT Kanpur, India-208016 -- Thanks & Regards Prave

Re: [gmx-users] parallelizing gromacs2018.4

irun command. > > Abhishek > > On Fri 23 Nov, 2018, 22:20 Mark Abraham, wrote: > > > Hi, > > > > Looks like nodes=1:ppn=20 sets the number of openmpi threads per rank to > be > > 20, on your cluster. Check the documentation for the cluster and/or talk > to

[gmx-users] parallelizing gromacs2018.4

Dear all I have successfully installed gromacs 2018.4 in local PC and HPC center (Without GPU) using these commands CMAKE_PREFIX_PATH=/home/sappidi/software/fftw-3.3.8 /home/sappidi/software/cmake-3.13.0/bin/cmake .. -DCMAKE_INCLUDE_PATH=/home/sappidi/software/fftw-3.3.8/include -DCMAKE_LIBRARY_PAT

Re: [gmx-users] DPD in Groamcs

> > -- > > Message: 1 > > Date: Mon, 23 Oct 2017 13:54:20 +0300 > > From: "Goga, N." > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] DPD in Groamcs > > Message-ID: > >

[gmx-users] DPD in Groamcs

Dear all is there any possibility of performing dissipative particle dynamics (DPD) in gromacs? Thanks in Advance Praveen -- 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.grom

[gmx-users] Scaling in gromacs

Dear GMX users In order to benchmark my simulation system I would like to know in gromacs which code scales linearly till 10K cores? Thanks Best Regards Praveen -- Thanks & Regards Dr. Praveen Kumar Sappidi, DST-National Postdoctoral Fellow Computational Nanoscience Lab Chemical Enginee

[gmx-users] Rotational correlation function for water

one from 5 ns production run (NVT ensemble) at 303 K. Thanks PRAVEEN KUMAR Research scholar INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH PUNE -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can

[gmx-users] rotational correlation function

Hi, I want to calculate rotational correlation time for a linear and non linear system. Could somebody help me to provide some input for calculating correlation function for linear and non linear molecule with explanation? Thanks Pravin -- Gromacs Users mailing list * Please search the archiv

[gmx-users] Calculation of non bonded interaction

Hi, I want to calculate non bonded interaction between an ion pair (say "A" and "B"). There are total 125 ion pairs in the system. How could I calculate the average non bonded interaction between one cation and anion in the system? Thanks, Pravin -- Gromacs Users mailing list * Please search

[gmx-users] Cluster size and aggregation number calculation

Hi, I am new to Gromacs. Can anybody help me to tell how to calculate cluster size and aggregation number in a liquid? Thanks Praveen -- 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 ht

Re: [gmx-users] Error in mdrun

earch 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

[gmx-users] pH based calculation

Dear Gromacs users, I want to do some pH based analysis. Can anybody suggest me right way to proceed further ? Thanks. PRAVEEN KUMAR Research scholar INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH PUNE -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

[gmx-users] Cavity size calculation

Dear all, I want to calculate cavity size inside some liquid in which CO2 is dissolved. Can somebody help me? Thanks. PRAVEEN KUMAR -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?