Re: [gmx-users] how to maintain planarity of graphene sheet

I checked. They are from AMBER. On Fri, Jan 15, 2016 at 5:50 AM, jagannath mondal wrote: > Hi Vitaly > > Unfortunately, the paper does not mention anything about whether the > forcefields for graphene were taken from OPLS or AMBER. > If I could get the topology file

Re: [gmx-users] Launch hybrid MPI/openMP run on multiple nodes

Hi, Thus you should find out how your system administrators intended you to use the resources. Mark On Fri, 15 Jan 2016 15:01 Szilárd Páll wrote: > Hi, > > Your job scheduler and/or MPI launcher is most likely to blame. The fact > that mdrun warns about the logical

Re: [gmx-users] Constraining positions according to B-factors

Hi Irem, Okay. First remove all bonded and nonbonded interactions, because these are what gives rise to the thermal fluctuations in a real crystal. So you would only need an [ atoms ] section and a section with [ position_restraints ]. You should be able to calculate a spring constants based on

Re: [gmx-users] Launch hybrid MPI/openMP run on multiple nodes

Hi, Your job scheduler and/or MPI launcher is most likely to blame. The fact that mdrun warns about the logical core (hardware thread) mismatch means that the OpenMP runtime thinks that you should be using one thread per rank. This typically means that the MPI launcher or job scheduler set an

[gmx-users] Membrane simulation npt problem

Good evening to everyone. I've an issue regarding a membrane simulation. I've downloaded an already equilibrated POPE/POPG membrane and, to test the system, I run an em, a 0.1 ns nvt and 1 ns npt simulation and everything was fine. Then, I've raised the cell lenght in the z direction and added a

Re: [gmx-users] Constraining positions according to B-factors

Hi, Thank you for your answer, I will try that. I realize it’s unphysical, but I want to compare certain properties of the protein to diffraction data. Just to double check: the values in [position_restraints] are in units of kJ/(mol*nm^2), right? Best, Irem > On Jan 15, 2016, at 9:47 AM,

[gmx-users] Out of memory error for g_density and trjconv

I've run an atomistic simulation of 2048 DOPC and 65,536 waters; so ~500,000 atoms in total. I'd like to produce an electron density plot of the bilayer so I tried to use g_density but immediately got the error message: Fatal error: Not enough memory. Failed to calloc -1082130432 elements of

Re: [gmx-users] Constraining positions according to B-factors

Hi Irem, I think it would be better to actually build and simulate a crystal and use the b-factors as a result of the model that allows you to do the comparison with the diffraction data. Applying position restraints to reproduce the b-factors will yield an unphysical system, from which I think

[gmx-users] Vesicle simulation crashed with dry martini force field

Hi,  I'm trying to simulate a large lipid vesicle ( ~ 100 nm in diameter) with the dry martini force field. The system consists of about 1.4 million particles. I'm trying to equilibrate the system in NVT ensemble in a simulation box with length 120 nm, using the timestep of 10 fs. The

Re: [gmx-users] Vesicle simulation crashed with dry martini force field

Why do you think that it's the domain decomposition load balancing causing the crash rather than the time-step? You say you ran successfully on less CPU cores with shorter time-step. What about less cores with 10 fs time-step? It would help if you share a less mis-formatted information or even a

[gmx-users] temperatures of residues

Dear all, I am going to calculate the temperature distribution inside a protein (temperatures of residues). Is there any command in gromacs to do that? Any suggestion is appreciated. Bests, Mohyeddin -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Membrane simulation npt problem

The problem is outside your parameter file. On Fri, Jan 15, 2016 at 3:56 PM, Marco Franzoi wrote: > Good evening to everyone. > > I've an issue regarding a membrane simulation. > I've downloaded an already equilibrated POPE/POPG membrane and, to test the > system,

[gmx-users] Launch hybrid MPI/openMP run on multiple nodes

Dear GMX developers and users, I have a cluster of 24 nodes, each having two 10-core intel CPUs. Gromacs 5.1 is compiled by using intel mpi (version 5.1.1) and mkl. I can successfully run a simulation by using pure MPI (480 MPI processes). But the performance is not good and the log file of

Re: [gmx-users] Electric field unit

Seems rational! Thank you very much David. On Thu, Jan 14, 2016 at 7:20 PM, mah maz wrote: > Thank you David but it still seems conflicting to me. V/nm and V/m are 100 > times different! If it is in V/nm then force unit should be wrong! > > On Thu, Jan 14, 2016 at 12:20 PM,