Re: [gmx-users] GMX 2018 regression tests: cufftPlanMany R2C plan failure (error code 5)

Just a quick update here regarding regression tests. On an old machine with a single puny GTX 960, the 2018 build passes all tests with Start 9: GpuUtilsUnitTests 9/39 Test #9: GpuUtilsUnitTests Passed5.64 sec Hope this is useful. Alex -- Gromacs Users mailing list *

Re: [gmx-users] Calculation of shape change of a protein during simulation

You can calculate the asphericity, for example. You just need the components of the gyration tensor which are given by gmx polystat, if my memory serves me right. There are several papers about this. A quick search on Google scholar will surely produce results. I would link the papers or the

[gmx-users] Calculation of shape change of a protein during simulation

Dear All, Is there any way to calculate the change in shape of a protein with respect to simulation time using GROMACS or VMD? By the use of the word 'shape', I mean to say 'spherical' or 'elliptical'; or more specifically the value of eccentricity of the protein wrt simulation time. My guess is

[gmx-users] the energy of the individual molecule

Suppose the trajectory of molecular system with interactions between all molecules. How is to obtain the time dependence of intramolecular energy of the given molecule with unique resname and the total energy of this molecule in the system including intermolecular interactions? -- Gromacs

[gmx-users] shear viscosity

Hi I want to obtain shear viscosity for ionic mixtures. I use the method Berk Hess gives in his paper, (J. Chem. Phy *116*, 209 (2002)). I would like to know if this is a better method, or the muller-plathe method (Phy. rev. E *59*, 5 (1999))? Best regards -- Gromacs Users mailing list *

Re: [gmx-users] tune_pme error with GROMACS 2018

> On 12. Feb 2018, at 22:44, Daniel Kozuch wrote: > > Carsten, > > I was hoping yo use tune_pme to optimize a REMD job across multiple nodes, > so I think I need it compiled with MPI (please let me know if that logic is > incorrect). Strictly speaking, tune_pme is a

Re: [gmx-users] Gromacs 2018 and GPU PME

Hi Szilard Thank you for answering. It did indeed show a significant improvement with, in particular, $ gmx mdrun -v -deffnm md -pme gpu -nb gpu -ntmpi 8 -ntomp 6 -npme 1 -gputasks 0001 I also now understand better how to control each individual simulation. Your point on maximizing

[gmx-users] Pulling protein from distance on membrane

Hi, I am trying to simulate a system in which a protein will be pulled from a distance and ultimately be put on a DPPC membrane system. I went through Lemkul's tutorial on membrane and successfully simulated protein-membrane systems before. In this case, I put the protein in the required

Re: [gmx-users] Atomtype 'sy' not found

Hi, There's also atomtypes.atp file in force fields that perhaps you need to adjust. Mark On Tue, Feb 13, 2018 at 10:40 AM wrote: > > Hi all, > >I was trying to pass a file through GROMACS using following command: > > > $gmx grompp -f minim_gmx5.mdp -c

[gmx-users] GROMOS96 53A6 with extended Berger lipid parameters (Prasanna)

Hi all, The force field combination used in GROMOS96 53A6 with extended Berger lipids contains L-J interaction cross-terms between protein lipid atom types? If so how abnormally high L-J interactions are tackled? In my case, to prepare the topology of my system (which contains proteins and

[gmx-users] Atomtype 'sy' not found

Hi all, I was trying to pass a file through GROMACS using following command: $gmx grompp -f minim_gmx5.mdp -c Solv.gro -p topol.top -o ions.tpr Then the follwing error popped up: Atomtype sy not found This is due to the presence of sulphur atom in my drug molecule Zafirlukast. I

[gmx-users] Atomtype sy not found error

Hi all, I was trying to pass a file through GROMACS using following command: $gmx grompp -f minim_gmx5.mdp -c Solv.gro -p topol.top -o ions.tpr Then the follwing error popped up: Atomtype sy not found This is due to the presence of sulphur atom in my drug molecule Zafirlukast. I