Re: [gmx-users] GETTING GOOD PERFORMANCE FROM MDRUN

Hi, You need to try all the possibilities and find out what combinations gives you the best. Further, I don't think you can achieve anything good with 8 logical processors for 'medium' protein or MD system. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] MM/PBSA

sure the below is my command line qsub /home/hauren32/Desktop/work/MM_PBSA_2.0/GMXPBSAtool/gmxpbsa0-1_TEST.pbs and the files i have are 1. npt.xtc 2.npt.tpr 2.index.ndx 3.topol.top 4. gdp.itp 5.protein.itp 2017-08-09 12:22 GMT+08:00 Amir Zeb : > can you please paste

[gmx-users] GETTING GOOD PERFORMANCE FROM MDRUN

Hi, How to get good (and fast) performance from mdrun through available 8 logical CPU cores? When I gave, gmx mdrun -ntmpi 2 -ntomp 4 -v -deffnm eq It seems to be slow, much slower than gmx mdrun -v -deffnm eq. Can anyone help? Thanks, Vidya R -- Gromacs Users mailing list * Please search

Re: [gmx-users] MM/PBSA

can you please paste your command line here? we can judge where you are wrong On Aug 9, 2017 12:50 PM, "Kingsley Theras Primus Dass ." < 105726...@gms.tcu.edu.tw> wrote: Hi everyone, I am trying to calculate the binding free energy between protein and ligand by using MM/PBSA. I included all

[gmx-users] MM/PBSA

Hi everyone, I am trying to calculate the binding free energy between protein and ligand by using MM/PBSA. I included all the .itp files. But when run the command, am getting an error saying "NO XTC" Could someone help me, what would be wrong, why such error occurs. i have pasted the error

Re: [gmx-users] vdw and Electrostatic energy

On 8/8/17 7:26 PM, Mohammad Zahidul Hossain Khan wrote: Dear Sir, Here is my part of the ligand energy. *Energies (kJ/mol)* * Bond Angle Proper Dih. Ryckaert-Bell.LJ-14* 3.27203e+019.31977e+012.74737e+004.46079e+01

Re: [gmx-users] convert .tpr to include energy groups

On 8/8/17 4:03 PM, Tushar Ranjan Moharana wrote: Hi All, I want to calculate interaction between 2 energy groups, which were not defined during the run. So I want to rerun and include both the energy groups while rerunning. This can be easily done by again assembling .tpr file from .gro, .top

Re: [gmx-users] (no subject)

On 8/8/17 1:06 PM, Sorour Hasani wrote: Im working on simulating a CYP2D6 with its cofactors (heme ) with GROMACS. When I run pdb2gmx, using CHARMM27 FF, I had no error. After looking in the literature, I found their corresponding parameters: I added the following fields in CHARMM file

[gmx-users] Problem with Ryzen, threads and core dumps?

Hi, I am trying to run a protein/water simulation using a new computer (Ryzen 1700X, Nvidia GTX 1070 running Ubuntu 17.04). I compiled GROMACS 2016.3 with gcc-5 (CUDA 8.0 complained that it only supports up to version 5) and -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON, otherwise

[gmx-users] convert .tpr to include energy groups

Hi All, I want to calculate interaction between 2 energy groups, which were not defined during the run. So I want to rerun and include both the energy groups while rerunning. This can be easily done by again assembling .tpr file from .gro, .top and .cpt file by grompp, but I donot have the .gro

Re: [gmx-users] Generating topology file for a long polymer chain

Thank you for your help! Best regards, Mahsa On Mon, Aug 7, 2017 at 4:35 PM, Justin Lemkul wrote: > > > On 8/6/17 8:35 PM, Mahsa E wrote: > >> Hello Justin, >> >> Thank you so much for your reply! >> >> I followed what you suggested. Please correct me if I misunderstood; >> >>

[gmx-users] (no subject)

Im working on simulating a CYP2D6 with its cofactors (heme ) with GROMACS. When I run pdb2gmx, using CHARMM27 FF, I had no error. After looking in the literature, I found their corresponding parameters: I added the following fields in CHARMM file ffbonded.itp [ bondtypes ] ; i j func b0 kb SG FE 1

Re: [gmx-users] clayff forcefield

Please don't reply to the entire digest; cut out only the relevant parts. On 8/8/17 2:37 AM, G R wrote: Hi, Thank you for your answer. yes, I know that I should make my own forcefield in my working directory, and I made this forcefield, but when I use x2top to generate itp file,