[gmx-users] Walls and PME

Hi, I'd like to simulate a membrane NPT with no pbc in the z direction. I understand I therefore need to use 2 walls. How does the pme work with walls? Is pme 2D only if I introduce wall(s)? Many thanks Sophia Wheeler PhD student Prof J Essex Group University of Southampton -- Gromacs

[gmx-users] Invallid order of atomtypes

Hi, I Have an itp file with the given first part: [ moleculetype ] ; Name nrexcl mols 3 [ atomtypes ] ; name at.num mass charge ptype sigma epsilon CR 6 12.0110 0.0 A 0.387541 0.230120 F 9 18.9984 0.0 A 0.290433 0.564840 SO2 16 32.0660 0.0 A 0.374177 1.966480 O2CM 8 15.9994 0.0 A

Re: [gmx-users] Constant Pressure just in z axis

Dear Christopher, Thank you for your help, How about the value of pressure along X/Y directions? does it matter the value of ref-p for X/Y while I use 0 for water compressibility in X/Y direction ? Respectfully, Iman On Wed, Oct 4, 2017 at 6:47 PM, Iman Ahmadabadi

Re: [gmx-users] peptide ligand

Dear Justin I performed NVT equilibration for 300 ps , it was done successfully. Yesterday I wanna do NPT equilibration , so used your npt.mdp file in the GROMACS tutorial and replaced energgroups and tc-groups by Protein and Protein water-ions, respectively, specified nstep = 15 , but when

Re: [gmx-users] How to recover a corrupted .edr file

Hi Christopher, can you regenerate the edr file using -rerun and your salvaged trajectory? That might be the easiest solution. Peter On 05-10-17 07:38, Christopher Neale wrote: > Dear users: > > > I recently experienced some corruption in a .xtc and a .edr file. Recovering > the .xtc was

Re: [gmx-users] problem of GB simulation

Most likely you do something wrong in energy minimization step: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.htmlMake sure you produce plot similar like in that page with your system before proceeding further with minimized system. On

Re: [gmx-users] MD simulation error : rRNA simulaion

In energy group you have given Potein and non-Protein and you are not simulation a protein but RNA. On Fri, Oct 6, 2017 at 12:53 AM, Hemant Arya wrote: > Dear gromacs, > Greetings > I am trying to run a NVT with the following command. > > My mdp file is below > >

Re: [gmx-users] How to recover a corrupted .edr file

Hi, On Thu, Oct 5, 2017 at 7:38 AM Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > Dear users: > > > I recently experienced some corruption in a .xtc and a .edr file. > Recovering the .xtc was pretty easy, I use gmx trjconv -b and -e to get the > part before the corruption and the

[gmx-users] Tabulated electrostatics not giving expected interactions

Hello, I have set up a simple simulation with 1000 water molecules and one K+ ion. The ion is fixed in place at the centre of the box and I expect to see clustering of the water molecules around the ion over time. Instead I only see a few weak interactions between one molecule and the ion and

Re: [gmx-users] Invallid order of atomtypes

Hi, You can't define a molecule before you define the force field. Mark On Thu, 5 Oct 2017 11:53 Sergio Manzetti wrote: > Hi, I Have an itp file with the given first part: > > > [ moleculetype ] > ; Name nrexcl > mols 3 > > [ atomtypes ] > ; name at.num mass

Re: [gmx-users] Constant Pressure just in z axis

I set the pressure the same. Not sure if it matters or not. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Iman Ahmadabadi Sent: 05 October 2017 03:16:01 To:

[gmx-users] legend in the pulling file (gmx 5.1.4)

Hi all, A quick question: What are the meaniings of the s1 , s1 and s2 legends in the pullf.xvg? @title "Pull COM" @xaxis label "Time (ps)" @yaxis label "Position (nm)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @

Re: [gmx-users] How to recover a corrupted .edr file

Thanks Peter. mdrun -rerun looks like a decent option. And thank you Mark for confirming the lack of skipping behavior. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Peter Kroon

[gmx-users] MD simulation error : rRNA simulaion

Dear gromacs, Greetings I am trying to run a NVT with the following command. My mdp file is below title = Protein-ligand complex NVT equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md; leap-frog integrator nsteps

Re: [gmx-users] Simulation in NPgT ensemble

a question - If I add a negative pressure in xy for the membrane stretching, using an approach: pcoupltype = semiisotropic tau_p 1 1 compressibility 4.5e-5 4.5e-5 ref_p -100 1 will it also increase the diffusion of the solvent along the xy plane of the membrane, thus mimicking effect of the