[gmx-users] Subject: Re: Group WAT referenced in the .mdp file was not found in the index file

Hi Justin, Thanks for your response, I am using a topology file constructed from amber tools ... -- *Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des Matériaux à l'état condensé, Laboratoire de Chimie Théorique et Spectroscopie MoléculaireUniversité de Tunis El

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 40

Hi Justin, Thanks for your response, I am using a topology file constructed from amber tools ... Le mar. 13 nov. 2018 à 01:04, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> a écrit : > Send gromacs.org_gmx-users mailing list submissions to >

[gmx-users] dssp excutable-error

Dear all I installed dssp software on ubuntu version 12.04 in the /usr/local/bin, when I run the following command "*sudo find / -name dssp*" it showed the mentioned pathway, but when I apply the following comand "*gmx do_dssp -f xtc -s tpr -o xpm -sc xvg -tu ns*" I confronted to this error:

Re: [gmx-users] Unable to generate .rtp file from gro and pdb file.

Hi, I didn't understand, what you exactly meant. Could you be more elaborate? Karpurmanjari On Sun, Nov 11, 2018 at 12:37 PM Karpurmanjari Kakati < ch18resch01...@iith.ac.in> wrote: > Hi > I tried doing the same, like you said. > 1. Copied the OPLS AA force field files to the directory, where

[gmx-users] Running GPU issue

Hi, To perform GPU with Gromacs does it require exclusive GPU card or Gromacs can share the video card with X-server? Thank you Dmytro -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

Re: [gmx-users] Building Gromacs

On 11/12/18 6:57 PM, paul buscemi wrote: This may be entirely misleading, but I have Gromacs 2018.3 loaded onto a SSD. This seems to be quite portable between machines I have access to ( during some builds ) ranging from an i5 4core, I7-8 core, i7-12 core and AMD 16 core 32 threads - all

Re: [gmx-users] atomtype OV not found

On 11/12/18 8:41 AM, Farial Tavakoli wrote: Dear Mark I changed the way of topology generating in AMBER. The peptidic ligand (has 2 phosphotyrosine residues) topology was generated using amber. all of the files that I have in my working directory are, Leaprc.ff99SB, Learc.phosaa10,

Re: [gmx-users] Group WAT referenced in the .mdp file was not found in the index file

On 11/12/18 7:14 AM, Rahma Dahmani wrote: Hi GMX users, i double checked in my topology and gro files that i am using the same moleculetype ( LIG and WAT) but when i run grompp for T equilibration i get an error message Group WAT referenced in the .mdp file was not found in the index

Re: [gmx-users] pdb2gmx fatal error

Dear Justin, Thank you for your full explanation. That made it all clear now. Kind regards, Ali > On 13 Nov 2018, at 00:57, Justin Lemkul wrote: > > > > On 11/8/18 1:37 PM, Ali Khodayari wrote: >> Dear Justin, >> >> Thank you for your response. Yet, I have not been able to solve the

Re: [gmx-users] Input file for energy minimization for solvated system: Error

On 11/11/18 3:04 PM, Neena Susan Eappen wrote: Hello GROMACS users, I was trying to create an input file for energy minimization of solvated system, using the following command: grompp -v -f minim.mdp -c protein-solvated.gro -p protein.top -o protein-EM-solvated.tpr Got the following

Re: [gmx-users] Expansion system after NVT Equilibrium in Gromacs

On 11/11/18 12:16 PM, yasmineso...@students.itb.ac.id wrote: i'm currently running a simulation protein in water using gromacs with force field gromos96 54a7. the protein structure that i used is from modeller. there is no problem untill the minimization step but the system is expanding

Re: [gmx-users] Building Gromacs

This may be entirely misleading, but I have Gromacs 2018.3 loaded onto a SSD. This seems to be quite portable between machines I have access to ( during some builds ) ranging from an i5 4core, I7-8 core, i7-12 core and AMD 16 core 32 threads - all with expected scaling in speed and all cores

Re: [gmx-users] pdb2gmx fatal error

On 11/8/18 1:37 PM, Ali Khodayari wrote: Dear Justin, Thank you for your response. Yet, I have not been able to solve the problem. The structure looks fine but gromacs is complaining about a dangling atom at one of the terminal ends, if I choose no terminal to be added. While, You can't

Re: [gmx-users] 4. Re: 5. Re: 3. Re: Strange pullx coordinates (PMF

On 11/8/18 12:12 PM, CROUZY Serge 119222 wrote: Hello Justin I still don't understand where Gromacs takes the x coordinates in the output pmf with g_wham If I run g_wham with tpr-files and pullf-files without the pullx-files -it tpr-files.dat -if pullf-files.dat I get a profile which means

Re: [gmx-users] DispErsion correction

On 11/8/18 10:58 AM, Farial Tavakoli wrote: Dear Justin and Dallas Thank you for your replying I have another problem in minimizing and NVT run of my complex, including a protein and a peptidic ligand which the ligand has 2 phosphotyrosine residues. I generated a topology file of ligand

[gmx-users] Building Gromacs

I was sure that a month ago when I started down the path of building and making Gromacs available for our user community, that I read a statement that whenever there is a hardware change, you need to rebuild Gromacs. I took this quite literally. So I assume that if hardware isn't identical (make,

[gmx-users] Insert Molecules Settings

I sent this message on Friday, but I didn't see it show up in my digest, so I'm trying again. Here's the previous text: Thanks all for your suggestions so far. I believe I've got things more or less functional but I want to refine how I'm constructing my initial simulation box. In

[gmx-users] Fwd: Gromacs 2018.3 with CUDA - segmentation fault (core dumped)

> > > Dear Benson and Szilard, > > Thank you for your interest. Benson, I will try to answer you questions > first: > 1) No, I have only tested 2018.3 so far. I just changed from Gromacs 5.1.4 > and these are my first tests. > 2) Not yet but I plan to do it. > 3) The results look reasonable after

Re: [gmx-users] Gromacs 2018.3 with CUDA - segmentation fault (core dumped)

> > Dear Benson and Szilard, > > Thank you for your interest. Benson, I will try to answer you questions > first: > 1) No, I have only tested 2018.3 so far. I just changed from Gromacs 5.1.4 > and these are my first tests. > 2) Not yet but I plan to do it. > 3) The results look reasonable after

[gmx-users] GROMACS 2018.4 patch release available

Hi GROMACS users, The official release of GROMACS 2018.4 is available! This release fixes several issues found since 2018.3. We encourage all users of the 2018 series to update to 2018.4. Please see the link to the release notes below for more details. You can find the code, documentation,

[gmx-users] atomtype OV not found

Dear Mark I changed the way of topology generating in AMBER. The peptidic ligand (has 2 phosphotyrosine residues) topology was generated using amber. all of the files that I have in my working directory are, Leaprc.ff99SB, Learc.phosaa10, frcmod.phosaa10, ligand.inpcrd, ligand.prmtop. The

[gmx-users] Group WAT referenced in the .mdp file was not found in the index file

Hi GMX users, i double checked in my topology and gro files that i am using the same moleculetype ( LIG and WAT) but when i run grompp for T equilibration i get an error message Group WAT referenced in the .mdp file was not found in the index file PS: i am not using an index file and i