Re: [gmx-users] Need to confirm parameters.

>>* Making bonds... *>>* Warning: Short Bond (5-1 = 0.025 nm) *>>* Warning: Long Bond (5-6 = 0.99084 nm) *>>* Warning: Long Bond (1-2 = 0.944378 nm) *>>* Warning: Long Bond (1-3 = 0.895661 nm) *>>* Warning: Long Bond (1-4 = 0.866986 nm) *>>* Warning: Long Bond (7-8 = 0.502204 nm) *>>* Warning:

[gmx-users] System Crashes

Hi Gromacs User, I am running a big system consisting of more than 5000 CG lipids molecules in each monolayer and these monolayers are separated by 133000 CG water molecules in a box 50*50*100. Everything run well up to equilibration (5 equilibration for 10ns ) but after 3 microsecond production

[gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04

Hi, I’ve tried installing GROMACS 2016.3 on Ubuntu 17.04. I’ve checked that gcc-6 and g++6 are installed, but when running cmake I get the following error: -- Performing Test CXX11_STDLIB_PRESENT - Failed CMake Error at cmake/gmxTestCXX11.cmake:139 (message): This version of GROMACS requires

Re: [gmx-users] atomname2types.n2t explanation

On 5/23/17 7:06 PM, Marcelo Depólo wrote: Hi Can someone explain what does each column on atomname2types.n2t mean? For gromos53a5 it is: H H0.408 1.008 1 O 0.1 O OA -0.674 15.9994 2 C 0.14 H 0.1 C CH3 0.000 15.0351 C 0.15 C CH0 0.266

Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

On 5/23/17 2:16 PM, Mohammad Hassan Khatami wrote: Thank Justin! I finished adding the new “residues” in the .rtp file. pdb2gmx runs straight forward. However, while doing energy minimizations, I get several errors like the ones below, arise: ERROR 2 [file topol.top, line 396]: No default

Re: [gmx-users] Need to confirm parameters.

On 5/23/17 8:03 AM, Sailesh Bataju wrote: The easiest thing to do (solving this issue and #1) is to create an isobutane .rtp entry and have pdb2gmx do all the work for you. It's very simple to do. -Justin Thank you sir, I've exactly followed your steps. I've created isobutane.rtp file

[gmx-users] atomname2types.n2t explanation

Hi Can someone explain what does each column on atomname2types.n2t mean? For gromos53a5 it is: H H0.408 1.008 1 O 0.1 O OA -0.674 15.9994 2 C 0.14 H 0.1 C CH3 0.000 15.0351 C 0.15 C CH0 0.266 12.0114 C 0.15 C 0.15 C 0.15

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 157, Issue 112

Thank you Mark and Szilárd! I have resorted to freezing the five atoms, and that has seemed to work, but of course at an energy toll. - Harrison On Tue, May 23, 2017 at 3:55 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to

Re: [gmx-users] Applying Dihedral Restraints to Polymer in GROMACS 5.1

Hi, It's a restraint - they move in the context of the force field and your extra potential. They're not frozen. Mark On Tue, May 23, 2017 at 7:49 PM Harry Ponce wrote: > Hello, > > I'm attempting to run an energy minimization on some high energy conformers > of a polymer

[gmx-users] mdrun failure

 Hi dear gmx-usersI am simulating gold surface- protein interaction by GOLP-CHARMM forcefield. after 30 ps equilibration, I started mdrun with some freeze atoms in gold surface and NVT ensemble in temp=300 k, but when mdrun starts, temperature reaches to 5.50769e+05. md.mdp file containe: title 

Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

Thank Justin! I finished adding the new “residues” in the .rtp file. pdb2gmx runs straight forward. However, while doing energy minimizations, I get several errors like the ones below, arise: ERROR 2 [file topol.top, line 396]: No default U-B types and ERROR 5 [file topol.top, line 550]:

[gmx-users] Applying Dihedral Restraints to Polymer in GROMACS 5.1

Hello, I'm attempting to run an energy minimization on some high energy conformers of a polymer dimer while restraining two dihedral angles pertaining to the five backbone carbons of interest. The literature and forums online are sparse when it comes to non-biochemical systems, and it seems as

Re: [gmx-users] (no subject)

Please do not post questions to the list "owner" (=admin) address. Post your questions to the users' list instead. Are you sure you are using the MPI-enabled GROMACS installation? Look in the mdrun log header (posting the link to the whole log uploaded to some sharing service might also help

Re: [gmx-users] Problem with accelerations

Mark, I'm not really sure what you mean by technique. I assume NEMD stands for Non-equilibrium MD? That is the case.. About my simulation: I am trying to simulate a fluid flow between surfaces. Two atomistic surfaces of gold atoms have been created at Z=0 and Z=z, where z is the top of the box.

Re: [gmx-users] Problem with accelerations

Hi, Which technique are you using for this? https://redmine.gromacs.org/issues/1354 speculates that this code is just broken, has been so for years, and should be removed given that nobody wishes to do the work to fix it ( :-( ) Mark On Tue, May 23, 2017 at 11:13 AM Kamps, M.

Re: [gmx-users] Regarding extending simulations with change in .mdp file

Hi, gmx grompp -f first -o first gmx mdrun -deffnm first gmx grompp -f second -o second gmx mdrun -deffnm second -cpi first does what I think you should want. You end up with output files named first.* and second.* which you can concatenate with trjconv or eneconv if what you plan to do with

[gmx-users] Graphene

Hi, I simulated the graphene by using this link "http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube;. Then, I solvated it in water using 'gmx solvate' command. But, when I wanted to add ions in the media by using 'gmx grompp' command, I got this error:...ERROR 6383 [file

Re: [gmx-users] Need to confirm parameters.

>The easiest thing to do >(solving this issue and #1) is to create an isobutane .rtp entry and have >pdb2gmx do all the work for you. It's very simple to do. > -Justin Thank you sir, I've exactly followed your steps. I've created isobutane.rtp file and modified residuetypes.dat file by adding

[gmx-users] mdrun failed

 Hi dear gmx-usersI want to simulate gold surface - proteininteraction by GOLP-CHARMM forcefield. In md step, after 7 ps , without anyreason mdrun failed. md.mdp contains: title   = gold cpp = cpp include =   ; RUN CONTROL PARAMETERS

[gmx-users] Problem with accelerations

Dear GMX users, I have some strange behaviour which I cannot explain. I want to accelerate atoms through my box at a certain velocity. Since I can only adjust the acceleration, I have to trial-and-error my way to the right accelerations. To do this, I create a smaller 'testing' simulation,

[gmx-users] Fw: mdrun failure

Hi dear gmx-usersIwant to simulate gold surface - protein interaction by GOLP-CHARMM forcefield.In md step, after 7 ps , without any reason mdrun failed. md.mdp contains: title                   = goldcpp                      =cppinclude                 =  ;RUN CONTROL PARAMETERSintegrator   

Re: [gmx-users] About using GLYCAM force field in Gromacs

you can try charmm-gui Weitong* Ren, PhD student* Laboratory of Biophysics Department of Physics *Nanjing University* Nanjing, Jiangsu, PR China 210093 tel : +86 025 8359 7226 *wt...@biophy.nju.edu.cn * On Tue, May 23, 2017 at 11:20 AM, 维维 wrote: > Dear