[gmx-users] Can't read xxx bytes of pullf.xvg to compute checksum

Dear users, I am running many (almost identical) simulations and every so often one crashes and I get this message. Initially I just deleted everything, started from scratch and the problem was solved. However it is starting to be annoying. Any idea what is happening? Is it an error of

Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

Hi Mark, *So, for the record, the actual issue is that GROMACS does not implement *some kind of tapering of non-bonded interactions that would apply between *particle pairs at short range? This is the extract from the supporting information of the paper I refer to that explains the issue

Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

Hi, I have now solved the problem. I have added a list of the 1-4 pairs within [ Pairs ] and it has led to the correct equilibrium bond length. Just as reference, information on the forcefield I am using is found in this paper: http://pubs.acs.org/doi/abs/10.1021/cm500365c Cheers, Amanda On

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 181

ohsen Ramezanpour) > 3. Re: Using SLLOD to find Viscosity (nishi kashyap) > 4. Deform a liquid (nishi kashyap) > 5. Anybody using Silica InterfaceFF on Gromacs? > (Diez Fernandez, Amanda) > 6. Re: Anybody using Silica InterfaceFF on Gromacs? (Alex) > > >--

[gmx-users] Anybody using Silica InterfaceFF on Gromacs?

Hi, I converted the InterfaceFF silica parameters to use in Gromacs (and to be compatible with the AMBER forcefield) and have gotten some problems, namely I am getting a slightly bigger equilibrium bond length than I should. I was wondering if there were other Gromacs users out there that have

Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

Hi Mark, Thanks. >mdrun will generally "make molecules whole" for -c, but otherwise doesn't >care. Implementing general triclininc 3D periodicity with domain >decomposition is a messy business. I am not using a triclinic unit cell (all angles are 90 in the input .pdb file). Wouldn¹t the

Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

<camnumarks3ogwr-gbht9gotmwburcobrbkjc1es+oy-c2ep...@mail.gmail.com> >Content-Type: text/plain; charset="UTF-8" > >Hi, > >On Wed, Jun 21, 2017 at 6:49 PM Diez Fernandez, Amanda < >amanda.die...@imperial.ac.uk> wrote: > >> Hi Justin, >&

Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

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[gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

Hi all, I am running a simulation and I find that the output coordinates of the simulation stored in “final_coordinates.gro” are distinctively different to any of the frames from “trajectory.gro” which I obtain from : trjconv –s file.tpr –f trajectory.xtc –o trajectory.gro When I visualise

[gmx-users] xx inconsistent shift check your topology

Dear Gromacs users, I am simulating a silica slab and get a warning stating there are “xx inconsistent shifts, check topology”. In my .mdp file I already have periodic-molecules=yes. Is this a common error? Do you recommend any approach to finding what causes it? Thank you, Amanda -- Gromacs

[gmx-users] NVE Temperature Drop ONLY When Applying Restraints

Dear Users, I was observing significant temperature drops in my system when switching from NPT equilibration to NVE. Within 1ns of the NVE run the temperature was so low the water was freezing. Trying to understand what was causing it, I have observed that it only occurs when I apply position

Re: [gmx-users] Diffusion coefficient water

Thanks Justin and Nikhil, 1) So in principle is it expected that results will be different and I should take my final value to be the average of, say, 10 simulations? 2)If so, the average over my simulations is not similar to the published average. They also use a unit cell of 216 molecules (I

[gmx-users] Diffusion coefficient water

Dear Gromacs users, I was trying to reproduce the published values for the diffusion coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using it in some of my simulations and I am failing to do so. More worryingly I get different results for different identical runs. I am using a

Re: [gmx-users] Segmentation Fault - Water on Substrate

coordinates that are broken across the former boundary, >you need to make them whole before your merge can work sanely. > >Mark > >On Sun, Jun 26, 2016 at 11:45 AM Diez Fernandez, Amanda < >amanda.die...@imperial.ac.uk> wrote: > >> Dear Gromacs users, >>

[gmx-users] Segmentation Fault - Water on Substrate

Dear Gromacs users, I am want to simulate water on a substrate. I have a water.pdb file with the coordinates of a cuboid of water and a substrate.pdb file with the coordinates of the substrate. The box dimensions along the x and y directions are identical for both files. I run two simulations

[gmx-users] md of only water - obtaining different pressure in the x , y and z directions

Hi, I am running a simulation which contains only water (using the spc216.gro coordinates and TIP3P model) in an NPT ensemble. I get different values for the average pressure in the x y and z directions. I am running the simulation for up to 10s in a 4nm side cube unit cell. I am using a Nose