[gmx-users] simulation Self assembly monolayers with OPLS-TIP3P (CPU and GUP)

Dear All, I am having a problem with OPLS FF. If I simulated SAMs layer with only water layer (without any peptide and protein) using OPLS-AA + TIP3P in GPU system that simulation is simulated properly there is no problem. But if the same system I run using MPI (parallel gromacs) then water molec

Re: [gmx-users] angle type error

It worked! Many thanks From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Wednesday, May 04, 2016 8:10 PM To: gmx-us...@gromacs.org Subject: Re: [g

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 12

thanks Justin Lemkul. i am using all units in Angstrom and kj/mole. soif the default of disre-fc is 1000 kj mol-1 nm-2 , what it would be in kj mol-1 A-2. i am trying to convert it through google but the number isn't looking satisfying. i know 1nm =10 A. Sana Saeed Khan, Research Assistant Chemo

Re: [gmx-users] angle type error

On 5/4/16 10:06 PM, Williams Miranda wrote: Dear Gromacs users I want to run a CG simulation of a protein membrane system using GROMACS. I prepared my system using the MARTINI MAKER of CHARMMM-GUI. I ran the first two minimization phases without trouble. But when I am to create the *tpr for t

[gmx-users] angle type error

Dear Gromacs users I want to run a CG simulation of a protein membrane system using GROMACS. I prepared my system using the MARTINI MAKER of CHARMMM-GUI. I ran the first two minimization phases without trouble. But when I am to create the *tpr for the first equilibration phase, I get the followi

Re: [gmx-users] RE GROMAC Free Energy Question on Topologies

I suggest to keep all discussions on the mailing list for the benefit of others. The masses are recommended to keep at one end state primarily to avoid bad interactions with constraints that may be involved in the transformation. In a thermodynamical cycle contributions from the masses should f

[gmx-users] two molecules in a single topology file

Dear Gromacs Users, I have a question to create a topology file with tabulated potentials. I have two molecules in coarse-grained beads. The first molecules are 5 beads and 3 types (A-B-C-B-A), and the second molecules are 3 beads and 2 types (D-E-D). A-B bond potential tabulated in table_b1

[gmx-users] urea simulation and hdb definition

Dear All, I am using amber99sb for simulation. While generating topology file for urea I am getting following error for hydrogens in urea molecule gmx pdb2gmx -f sol-d.pdb -o protein1.gro -p topol1.top -ignh - WARNING: atom H11 is missing in residue URE 1914 in the pdb file You might ne

Re: [gmx-users] How to Compile tools without mpi ?

Should I compile 2 versions of Gromacs, one with and another without mpi ? FR. -Message d'origine- De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part de Mark Abraham Envoyé : mercredi 4 mai 2016 16:58 À : gmx-us..

Re: [gmx-users] How to Compile tools without mpi ?

Hi, Per the install guide, don't use an MPI wrapper compiler, and/or don't use -DGMX_MPI=on cmake option. Mark On Wed, May 4, 2016 at 4:35 PM Chalaoux, Francois-Regis < francois-regis.chala...@evotec.com> wrote: > Hi, > > How to compile tools without mpi (i.e. do_dssp) ? > > FR > -- > Gromacs U

[gmx-users] How to Compile tools without mpi ?

Hi, How to compile tools without mpi (i.e. do_dssp) ? FR -- 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 * For (un)subscribe requests visit

Re: [gmx-users] do_dssp strange reaction

On 5/4/16 9:20 AM, Chalaoux, Francois-Regis wrote: Hi everybody, Trying to use do_dssp_mpi for my MD I got an error described below. I gave "-ver 2" for dssp 2.0.4 but nothing changed. This is a real pain in the neck since a week to debug this message. Any tracks Guys ? The usual tips are

[gmx-users] do_dssp strange reaction

Hi everybody, Trying to use do_dssp_mpi for my MD I got an error described below. I gave "-ver 2" for dssp 2.0.4 but nothing changed. This is a real pain in the neck since a week to debug this message. Any tracks Guys ? FRC Config: Linux Centos 6.7 Gromacs mpi 5.04 == CMD and Erro

Re: [gmx-users] restarts

On 5/4/16 8:32 AM, ingram wrote: Dear GROMITES I have run a simulation that will take longer than a day (longer than my allowed time for one simulaiton on the cluster) I ran the command mdrun -deffnm md_golp Now I'm not sure which .cpt file to use. Two are produced, one called state.cpt and

[gmx-users] restarts

Dear GROMITES I have run a simulation that will take longer than a day (longer than my allowed time for one simulaiton on the cluster) I ran the command mdrun -deffnm md_golp Now I'm not sure which .cpt file to use. Two are produced, one called state.cpt and one called md_golp.cpt. They are

Re: [gmx-users] persistent jumps in trajectories

On 5/4/16 6:12 AM, morpheus wrote: Hi, I'm having problems getting jumps out of my trajectories. Usually I follow the suggestion of the Gromacs website ( http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions) and convert my trajectories with the perl script below: remov

Re: [gmx-users] restraints definition in mdp

On 5/4/16 6:12 AM, Sana Saeed wrote: but i didnt specified force constant for distance ..is that fine? see my topology file contents following: Sorry; misread "distance" as "dihedral." Yes, there are .mdp options for distance restraints. http://manual.gromacs.org/documentation/5.1.2/user

[gmx-users] persistent jumps in trajectories

Hi, I'm having problems getting jumps out of my trajectories. Usually I follow the suggestion of the Gromacs website ( http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions) and convert my trajectories with the perl script below: remove water, make it whole, cluster, nojump

Re: [gmx-users] restraints definition in mdp

On 5/4/16 4:08 AM, Sana Saeed wrote: hi gromacs experts i have applied distance, angle and dihedral restraints to my ligand in a protein's pocket so that it doesnt roam around when i turn off all interactions during simulation. do i need to mention about these restraints in the mdp file? i a

Re: [gmx-users] pdb2gmx -ignh

On 5/4/16 5:02 AM, Alexander Alexander wrote: Dear GMX user, As you know, naming the Hydrogen atom differently in different FF and in .pdb or .gro file brings lots of problems in the "gmx pdb2gmx". I also met the issue when I wanted to convert my self-made (by Avogadro) heptapeptide.pdb to hep

[gmx-users] pdb2gmx -ignh

Dear GMX user, As you know, naming the Hydrogen atom differently in different FF and in .pdb or .gro file brings lots of problems in the "gmx pdb2gmx". I also met the issue when I wanted to convert my self-made (by Avogadro) heptapeptide.pdb to heptapeptide.gro file. I could get rid of them using

[gmx-users] restraints definition in mdp

hi gromacs experts i have applied distance, angle and dihedral restraints to my ligand in a protein's pocket so that it doesnt roam around when i turn off all interactions during simulation. do i need to mention about these restraints in the mdp file? i am using gromacs 5.0 and 5.1. i have used